Alignments for a candidate for glcB in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Alignments for a candidate for glcB in Sinorhizobium meliloti 1021

Align Malate synthase G (EC 2.3.3.9) (characterized)
to candidate SMc02581 SMc02581 malate synthase G

Query= reanno::psRCH2:GFF353
         (726 letters)



>FitnessBrowser__Smeli:SMc02581
          Length = 723

 Score =  982 bits (2539), Expect = 0.0
 Identities = 473/723 (65%), Positives = 580/723 (80%), Gaps = 2/723 (0%)

Query: 3   ERVQVGGLQVAKVLYDFVNNEAIPGTGVDAAAFWAGADSVIHDLAPKNRALLAKRDDLQA 62
           +RV+  GLQ+   L+ F+  EA+PGTGVDA  F++    ++HDL PKNRALL KRD+LQA
Sbjct: 2   DRVEKYGLQIDAGLHRFLVEEAMPGTGVDADRFFSAFSDLVHDLGPKNRALLVKRDELQA 61

Query: 63  QIDAWHQARAGQAHDAVAYKSFLQEIGYLLPEAEDFQATTENVDEEIARMAGPQLVVPIM 122
           ++D W++   G   D  AY++FL+EIGYLLPE  DF  +T NVD EIA +AGPQLVVP+M
Sbjct: 62  RLDGWYREH-GAPVDMEAYEAFLREIGYLLPEGPDFYVSTANVDSEIATIAGPQLVVPVM 120

Query: 123 NARFALNAANARWGSLYDALYGTDAISEADGASKGPGYNEIRGNKVIAYARNFLNEAAPL 182
           NAR+ALNAANARWGSLYDALYGTDAI+E DGA +G GYN  RG KVIA+AR FL+ +APL
Sbjct: 121 NARYALNAANARWGSLYDALYGTDAIAETDGAERGKGYNPKRGAKVIAWAREFLDASAPL 180

Query: 183 ETGSHVDSTGYRIEGGKLVVSLKDGSTTGLKNPAQLQGFQGEASAPIAVLLKNNGIHFEI 242
             G   D+  + +EG  L V+L DG+ +  +N  Q  G+ G+ +AP  ++L+ NG+H  I
Sbjct: 181 AAGRWSDAKSFSVEGATLTVTLADGTKSAPRNSVQFAGYAGDPAAPSEIVLRRNGLHIVI 240

Query: 243 QIDPASPIGQTDAAGVKDILMESALTTIMDCEDSIAAVDADDKTVVYRNWLGLMKGDLVE 302
            +D  +PIG+ DAAG+ D+++ESA+TTIMDCEDSIAAVDA+DK +VYRNWLGLMKGDL E
Sbjct: 241 VLDATTPIGKADAAGISDVVLESAITTIMDCEDSIAAVDAEDKVLVYRNWLGLMKGDLEE 300

Query: 303 ELEKGGKRITRAMNPDRVYTKADGNGELTLHGRSLLFIRNVGHLMTNDAILDKEGNEVPE 362
           E+ KGG+  TR +NPDR YT  DG   LTL GRSL+ +RNVGHLMTN A+LD++G EVPE
Sbjct: 301 EVTKGGRAFTRRLNPDRAYTAPDG-ATLTLPGRSLMLVRNVGHLMTNPAVLDRDGEEVPE 359

Query: 363 GIMDGLFTSLIAVHNLNGNTSRKNTRTGSMYIVKPKMHGPEEVAFATELFGRVEDVLGLP 422
           G+MD + T+LIA+H++  N  R N+R+GSMY+VKPKMHGPEEVAFA E+F RVE  LGLP
Sbjct: 360 GLMDAMVTALIALHDIGRNGRRANSRSGSMYVVKPKMHGPEEVAFACEIFARVEAALGLP 419

Query: 423 RNTLKVGIMDEERRTTINLKACIKEARERVVFINTGFLDRTGDEIHTSMEAGPMVRKAAM 482
            N +K+GIMDEERRTT+NLK CI+ ARERVVFINTGFLDRTGDEIHTSMEAGPM+RK  M
Sbjct: 420 ANAMKMGIMDEERRTTVNLKECIRAARERVVFINTGFLDRTGDEIHTSMEAGPMIRKGDM 479

Query: 483 KAEKWISAYENNNVDVGLACGLQGKAQIGKGMWAMPDLMAAMLEQKVGHPMAGANTAWVP 542
           K   WISAYEN NVDVGL CGL G AQIGKGMWAMPDLMAAMLEQK+ HP AGANTAWVP
Sbjct: 480 KQAPWISAYENWNVDVGLECGLSGHAQIGKGMWAMPDLMAAMLEQKIVHPKAGANTAWVP 539

Query: 543 SPTAATLHAMHYHKIDVQARQVELAKREKASIDDILTIPLAQDTNWSEEEKRNELDNNSQ 602
           SPTAATLHA HYH+++V   Q  L  R +A + DIL++P+A   NW+EEE + ELDNN+Q
Sbjct: 540 SPTAATLHATHYHRVNVAEVQASLKSRTRAKLADILSVPVAARPNWTEEEIQRELDNNAQ 599

Query: 603 GILGYMVRWVEQGVGCSKVPDINDIALMEDRATLRISSQHVANWMRHGVVTKDQVVESLK 662
           GILGY+VRWV+QGVGCSKVPDIN++ LMEDRATLRIS+QH+ANW+ HG+V++ Q+VE+++
Sbjct: 600 GILGYVVRWVDQGVGCSKVPDINNVGLMEDRATLRISAQHMANWLHHGIVSEAQIVETMQ 659

Query: 663 RMAPVVDRQNQGDPLYRPMAPDFDNSVAFQAALELVLEGTKQPNGYTEPVLHRRRREFKA 722
           RMA +VD QN GDP Y+PMA  F+ S+AFQAAL+LVL+G +QPNGYTEPVLHRRR E KA
Sbjct: 660 RMAAIVDGQNAGDPNYQPMAGRFEESIAFQAALDLVLKGREQPNGYTEPVLHRRRLELKA 719

Query: 723 KNG 725
           K G
Sbjct: 720 KQG 722


Lambda     K      H
   0.316    0.133    0.386 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 1481
Number of extensions: 59
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 726
Length of database: 723
Length adjustment: 40
Effective length of query: 686
Effective length of database: 683
Effective search space:   468538
Effective search space used:   468538
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 55 (25.8 bits)

Align candidate SMc02581 SMc02581 (malate synthase G)
to HMM TIGR01345 (glcB: malate synthase G (EC 2.3.3.9))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR01345.hmm
# target sequence database:        /tmp/gapView.4896.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01345  [M=721]
Accession:   TIGR01345
Description: malate_syn_G: malate synthase G
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
          0 1177.3   0.0          0 1177.1   0.0    1.0  1  lcl|FitnessBrowser__Smeli:SMc02581  SMc02581 malate synthase G


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SMc02581  SMc02581 malate synthase G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1177.1   0.0         0         0       2     720 ..       3     720 ..       2     721 .. 0.99

  Alignments for each domain:
  == domain 1  score: 1177.1 bits;  conditional E-value: 0
                           TIGR01345   2 rvdagrlqvakklkdfveeevlpgtgvdaekfwsgfdeivrdlapenrellakrdeiqaaideyhrknkgvidke 76 
                                         rv++ +lq+++ l++f+ ee++pgtgvda+ f+s+f+++v+dl p+nr ll krde+qa +d ++r+  +++d e
  lcl|FitnessBrowser__Smeli:SMc02581   3 RVEKYGLQIDAGLHRFLVEEAMPGTGVDADRFFSAFSDLVHDLGPKNRALLVKRDELQARLDGWYREHGAPVDME 77 
                                         577889********************************************************************* PP

                           TIGR01345  77 ayksflkeigylveepervtietenvdseiasqagpqlvvpvlnaryalnaanarwgslydalygsnvipeedga 151
                                         ay+ fl+eigyl +e     + t nvdseia+ agpqlvvpv+naryalnaanarwgslydalyg+++i+e+dga
  lcl|FitnessBrowser__Smeli:SMc02581  78 AYEAFLREIGYLLPEGPDFYVSTANVDSEIATIAGPQLVVPVMNARYALNAANARWGSLYDALYGTDAIAETDGA 152
                                         *************************************************************************** PP

                           TIGR01345 152 ekgkeynpkrgekviefarefldeslplesgsyadvvkykivdkklavqlesgkvtrlkdeeqfvgyrgdaadpe 226
                                         e+gk ynpkrg kvi++arefld s pl +g + d+ ++++    l+v+l +g +   ++  qf gy gd a+p+
  lcl|FitnessBrowser__Smeli:SMc02581 153 ERGKGYNPKRGAKVIAWAREFLDASAPLAAGRWSDAKSFSVEGATLTVTLADGTKSAPRNSVQFAGYAGDPAAPS 227
                                         *************************************************************************** PP

                           TIGR01345 227 villktnglhielqidarhpigkadkakvkdivlesaittildcedsvaavdaedkvlvyrnllglmkgtlkekl 301
                                          i+l++nglhi + +da+ pigkad a++ d+vlesaitti+dceds+aavdaedkvlvyrn+lglmkg+l+e++
  lcl|FitnessBrowser__Smeli:SMc02581 228 EIVLRRNGLHIVIVLDATTPIGKADAAGISDVVLESAITTIMDCEDSIAAVDAEDKVLVYRNWLGLMKGDLEEEV 302
                                         *************************************************************************** PP

                           TIGR01345 302 ekngriikrklnedrsytaangeelslhgrsllfvrnvghlmtipviltdegeeipegildgvltsvialydlkv 376
                                         +k gr ++r+ln dr+yta++g +l+l+grsl++vrnvghlmt+p++l+ +gee+peg++d+++t++ial+d+ +
  lcl|FitnessBrowser__Smeli:SMc02581 303 TKGGRAFTRRLNPDRAYTAPDGATLTLPGRSLMLVRNVGHLMTNPAVLDRDGEEVPEGLMDAMVTALIALHDIGR 377
                                         *************************************************************************** PP

                           TIGR01345 377 qnklrnsrkgsvyivkpkmhgpeevafanklftriedllglerhtlkvgvmdeerrtslnlkaciakvkervafi 451
                                         +++  nsr gs+y+vkpkmhgpeevafa ++f+r+e  lgl+ +++k+g+mdeerrt++nlk ci  ++erv+fi
  lcl|FitnessBrowser__Smeli:SMc02581 378 NGRRANSRSGSMYVVKPKMHGPEEVAFACEIFARVEAALGLPANAMKMGIMDEERRTTVNLKECIRAARERVVFI 452
                                         *************************************************************************** PP

                           TIGR01345 452 ntgfldrtgdeihtsmeagamvrkadmksapwlkayernnvaagltcglrgkaqigkgmwampdlmaemlekkgd 526
                                         ntgfldrtgdeihtsmeag+m+rk+dmk apw++aye+ nv+ gl cgl g+aqigkgmwampdlma mle+k+ 
  lcl|FitnessBrowser__Smeli:SMc02581 453 NTGFLDRTGDEIHTSMEAGPMIRKGDMKQAPWISAYENWNVDVGLECGLSGHAQIGKGMWAMPDLMAAMLEQKIV 527
                                         *************************************************************************** PP

                           TIGR01345 527 qlragantawvpsptaatlhalhyhrvdvqkvqkeladaerraelkeiltipvaentnwseeeikeeldnnvqgi 601
                                          ++agantawvpsptaatlha+hyhrv+v +vq++l++  +ra+l +il +pva   nw+eeei++eldnn+qgi
  lcl|FitnessBrowser__Smeli:SMc02581 528 HPKAGANTAWVPSPTAATLHATHYHRVNVAEVQASLKSR-TRAKLADILSVPVAARPNWTEEEIQRELDNNAQGI 601
                                         ************************************998.899******************************** PP

                           TIGR01345 602 lgyvvrwveqgigcskvpdihnvalmedratlrissqhlanwlrhgivskeqvleslermakvvdkqnagdeayr 676
                                         lgyvvrwv+qg+gcskvpdi nv lmedratlris+qh+anwl hgivs  q++e+++rma +vd qnagd+ y+
  lcl|FitnessBrowser__Smeli:SMc02581 602 LGYVVRWVDQGVGCSKVPDINNVGLMEDRATLRISAQHMANWLHHGIVSEAQIVETMQRMAAIVDGQNAGDPNYQ 676
                                         *************************************************************************** PP

                           TIGR01345 677 pmadnleasvafkaakdlilkgtkqpsgytepilharrlefkek 720
                                         pma+ +e+s+af+aa dl+lkg +qp+gytep+lh+rrle k+k
  lcl|FitnessBrowser__Smeli:SMc02581 677 PMAGRFEESIAFQAALDLVLKGREQPNGYTEPVLHRRRLELKAK 720
                                         ******************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (721 nodes)
Target sequences:                          1  (723 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.04
# Mc/sec: 12.49
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
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Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for catabolism of small carbon sources