Alignments for a candidate for glcB in Marinobacter adhaerens HP15

GapMind for catabolism of small carbon sources

Alignments for a candidate for glcB in Marinobacter adhaerens HP15

Align Malate synthase G (EC 2.3.3.9) (characterized)
to candidate GFF2238 HP15_2188 malate synthase G

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



>FitnessBrowser__Marino:GFF2238
          Length = 726

 Score = 1020 bits (2638), Expect = 0.0
 Identities = 501/726 (69%), Positives = 593/726 (81%), Gaps = 2/726 (0%)

Query: 1   MTERVQVGGLQVAKVLYDFVNNEAIPGTGVDAAAFWAGADSVIHDLAPKNRALLAKRDDL 60
           MTERVQVGG+QVAK LYDFVNNEAIPGTG+DA  FWA  D ++++LAP+NR LLAKRD +
Sbjct: 1   MTERVQVGGIQVAKNLYDFVNNEAIPGTGIDADKFWAEFDKIVNELAPRNRELLAKRDAI 60

Query: 61  QAQIDAWHQARAGQAHDAVAYKSFLQEIGYLLPEAEDFQATTENVDEEIARMAGPQLVVP 120
           Q ++D+W++   GQ  D   YKSFL++IGYL+ E  +F+ +T NVD E+A MAGPQLVVP
Sbjct: 61  QEKMDSWNRDHKGQKLDMGEYKSFLKDIGYLVDEPSEFKISTSNVDPEVATMAGPQLVVP 120

Query: 121 IMNARFALNAANARWGSLYDALYGTDAISEADGASKGPGYNEIRGNKVIAYARNFLNEAA 180
           IMNARFALNAANARWGSLYDALYGTDAISE DGA KG GYN +RG KVI +ARN L+ +A
Sbjct: 121 IMNARFALNAANARWGSLYDALYGTDAISEEDGAEKGRGYNPVRGAKVIEWARNLLDSSA 180

Query: 181 PLETGSHVDSTGYRIEGGKLVVSLKDGSTTGLKNPAQLQGFQGEASAPIAVLLKNNGIHF 240
           PL +GSH D+  Y + GGKLVV L++G +TGLK+ A   G+ G A AP  VLL  NG+HF
Sbjct: 181 PLASGSHKDAAKYVVVGGKLVVKLQNGESTGLKDEAGFVGYTGAADAPTGVLLVKNGMHF 240

Query: 241 EIQIDPASPIGQTDAAGVKDILMESALTTIMDCEDSIAAVDADDKTVVYRNWLGLMKGDL 300
           EIQID   PIG+ D A VKD+LMESALTTIMDCEDS+AAVDADDK + YRNWLGLMKGDL
Sbjct: 241 EIQIDATHPIGKDDGAHVKDVLMESALTTIMDCEDSVAAVDADDKALAYRNWLGLMKGDL 300

Query: 301 VEELEKGGKRITRAMNPDRVYTKADGNGELTLHGRSLLFIRNVGHLMTNDAILDKEGNEV 360
            E  EKGG+++TR MN DR YT ADG+ EL+L GRSL+FIRNVGHLMTN AIL K+GNEV
Sbjct: 301 QETFEKGGEQLTRKMNADRTYTAADGS-ELSLKGRSLMFIRNVGHLMTNPAILLKDGNEV 359

Query: 361 PEGIMDGLFTSLIAVHNLNGNTSRKNTRTGSMYIVKPKMHGPEEVAFATELFGRVEDVLG 420
           PEG+MDGL TSLIA+H++ GN   +N+  GSMYIVKPKMHGPEEVAF  E FGRVED L 
Sbjct: 360 PEGLMDGLITSLIAIHDMKGNGKFQNSTKGSMYIVKPKMHGPEEVAFTNEFFGRVEDALS 419

Query: 421 LPRNTLKVGIMDEERRTTINLKACIKEARERVVFINTGFLDRTGDEIHTSMEAGPMVRKA 480
           LPR +LKVGIMDEERRTT+NLKACI  A+ER VFINTGFLDRTGDEIHTSME GP +RK 
Sbjct: 420 LPRFSLKVGIMDEERRTTVNLKACIHAAKERAVFINTGFLDRTGDEIHTSMELGPFIRKG 479

Query: 481 AMKAEKWISAYENNNVDVGLACGLQGKAQIGKGMWAMPDLMAAMLEQKVGHPMAGANTAW 540
           AMK   WI+AYE  NVD+GL  G +G AQIGKGMWAMPDLMA MLE K+GHP AGANTAW
Sbjct: 480 AMKQATWINAYEQWNVDIGLETGFRGVAQIGKGMWAMPDLMAGMLEAKIGHPKAGANTAW 539

Query: 541 VPSPTAATLHAMHYHKIDVQARQVELAKREKASIDDILTIPLAQD-TNWSEEEKRNELDN 599
           VPSPTAATLHA HYH++ V   Q +L  R +A++DDILT+P+  D  + S E+ + ELDN
Sbjct: 540 VPSPTAATLHATHYHQVSVADVQKQLESRTRAALDDILTVPVMDDPASLSAEDIQQELDN 599

Query: 600 NSQGILGYMVRWVEQGVGCSKVPDINDIALMEDRATLRISSQHVANWMRHGVVTKDQVVE 659
           N+QGILGY+VRW++QGVGCSKVPDIND+ LMEDRATLRI+SQ +ANW+ HG+ ++DQ++E
Sbjct: 600 NAQGILGYVVRWIDQGVGCSKVPDINDVGLMEDRATLRIASQLLANWLHHGICSEDQIME 659

Query: 660 SLKRMAPVVDRQNQGDPLYRPMAPDFDNSVAFQAALELVLEGTKQPNGYTEPVLHRRRRE 719
           ++KRMA VVD+QN GD  YRPMA +FD+SVAFQAAL+LVL+G +QPNGYTEP+LH  R +
Sbjct: 660 TMKRMAAVVDKQNAGDSAYRPMAGNFDDSVAFQAALDLVLKGREQPNGYTEPLLHAYRLK 719

Query: 720 FKAKNG 725
            KAK G
Sbjct: 720 AKAKYG 725


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: 1471
Number of extensions: 46
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: 726
Length adjustment: 40
Effective length of query: 686
Effective length of database: 686
Effective search space:   470596
Effective search space used:   470596
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 GFF2238 HP15_2188 (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.12341.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 1210.5   0.7          0 1210.3   0.7    1.0  1  lcl|FitnessBrowser__Marino:GFF2238  HP15_2188 malate synthase G


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF2238  HP15_2188 malate synthase G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1210.3   0.7         0         0       2     720 ..       4     723 ..       3     724 .. 0.99

  Alignments for each domain:
  == domain 1  score: 1210.3 bits;  conditional E-value: 0
                           TIGR01345   2 rvdagrlqvakklkdfveeevlpgtgvdaekfwsgfdeivrdlapenrellakrdeiqaaideyhrknk.gvidk 75 
                                         rv++g++qvak+l+dfv++e++pgtg+da+kfw++fd+iv++lap+nrellakrd iq  +d + r+ k    d 
  lcl|FitnessBrowser__Marino:GFF2238   4 RVQVGGIQVAKNLYDFVNNEAIPGTGIDADKFWAEFDKIVNELAPRNRELLAKRDAIQEKMDSWNRDHKgQKLDM 78 
                                         7899*****************************************************************4457** PP

                           TIGR01345  76 eayksflkeigylveepervtietenvdseiasqagpqlvvpvlnaryalnaanarwgslydalygsnvipeedg 150
                                           yksflk+igylv+ep + +i t nvd e+a+ agpqlvvp++nar+alnaanarwgslydalyg+++i+eedg
  lcl|FitnessBrowser__Marino:GFF2238  79 GEYKSFLKDIGYLVDEPSEFKISTSNVDPEVATMAGPQLVVPIMNARFALNAANARWGSLYDALYGTDAISEEDG 153
                                         *************************************************************************** PP

                           TIGR01345 151 aekgkeynpkrgekviefarefldeslplesgsyadvvkykivdkklavqlesgkvtrlkdeeqfvgyrgdaadp 225
                                         aekg+ ynp+rg kvie+ar++ld+s pl sgs++d+ ky +v +kl+v+l++g+ t lkde+ fvgy+g a +p
  lcl|FitnessBrowser__Marino:GFF2238 154 AEKGRGYNPVRGAKVIEWARNLLDSSAPLASGSHKDAAKYVVVGGKLVVKLQNGESTGLKDEAGFVGYTGAADAP 228
                                         *************************************************************************** PP

                           TIGR01345 226 evillktnglhielqidarhpigkadkakvkdivlesaittildcedsvaavdaedkvlvyrnllglmkgtlkek 300
                                         + +ll +ng+h e+qida+hpigk+d a+vkd+++esa+tti+dcedsvaavda+dk l yrn+lglmkg+l+e+
  lcl|FitnessBrowser__Marino:GFF2238 229 TGVLLVKNGMHFEIQIDATHPIGKDDGAHVKDVLMESALTTIMDCEDSVAAVDADDKALAYRNWLGLMKGDLQET 303
                                         *************************************************************************** PP

                           TIGR01345 301 lekngriikrklnedrsytaangeelslhgrsllfvrnvghlmtipviltdegeeipegildgvltsvialydlk 375
                                         +ek g +++rk+n dr+ytaa+g+elsl+grsl+f+rnvghlmt+p+il ++g+e+peg++dg++ts+ia++d+k
  lcl|FitnessBrowser__Marino:GFF2238 304 FEKGGEQLTRKMNADRTYTAADGSELSLKGRSLMFIRNVGHLMTNPAILLKDGNEVPEGLMDGLITSLIAIHDMK 378
                                         *************************************************************************** PP

                           TIGR01345 376 vqnklrnsrkgsvyivkpkmhgpeevafanklftriedllglerhtlkvgvmdeerrtslnlkaciakvkervaf 450
                                          ++k++ns kgs+yivkpkmhgpeevaf+n++f+r+ed l l+r +lkvg+mdeerrt++nlkaci+ +ker +f
  lcl|FitnessBrowser__Marino:GFF2238 379 GNGKFQNSTKGSMYIVKPKMHGPEEVAFTNEFFGRVEDALSLPRFSLKVGIMDEERRTTVNLKACIHAAKERAVF 453
                                         *************************************************************************** PP

                           TIGR01345 451 intgfldrtgdeihtsmeagamvrkadmksapwlkayernnvaagltcglrgkaqigkgmwampdlmaemlekkg 525
                                         intgfldrtgdeihtsme g+++rk+ mk a+w++aye+ nv+ gl +g+rg aqigkgmwampdlma mle k+
  lcl|FitnessBrowser__Marino:GFF2238 454 INTGFLDRTGDEIHTSMELGPFIRKGAMKQATWINAYEQWNVDIGLETGFRGVAQIGKGMWAMPDLMAGMLEAKI 528
                                         *************************************************************************** PP

                           TIGR01345 526 dqlragantawvpsptaatlhalhyhrvdvqkvqkeladaerraelkeiltipvaen.tnwseeeikeeldnnvq 599
                                         + ++agantawvpsptaatlha+hyh+v v  vqk+l +  +ra l++ilt+pv ++ +  s+e+i++eldnn+q
  lcl|FitnessBrowser__Marino:GFF2238 529 GHPKAGANTAWVPSPTAATLHATHYHQVSVADVQKQLESR-TRAALDDILTVPVMDDpASLSAEDIQQELDNNAQ 602
                                         *************************************988.8999********98753899************** PP

                           TIGR01345 600 gilgyvvrwveqgigcskvpdihnvalmedratlrissqhlanwlrhgivskeqvleslermakvvdkqnagdea 674
                                         gilgyvvrw++qg+gcskvpdi +v lmedratlri+sq lanwl hgi s +q++e+++rma vvdkqnagd a
  lcl|FitnessBrowser__Marino:GFF2238 603 GILGYVVRWIDQGVGCSKVPDINDVGLMEDRATLRIASQLLANWLHHGICSEDQIMETMKRMAAVVDKQNAGDSA 677
                                         *************************************************************************** PP

                           TIGR01345 675 yrpmadnleasvafkaakdlilkgtkqpsgytepilharrlefkek 720
                                         yrpma+n+++svaf+aa dl+lkg +qp+gytep+lha+rl+ k+k
  lcl|FitnessBrowser__Marino:GFF2238 678 YRPMAGNFDDSVAFQAALDLVLKGREQPNGYTEPLLHAYRLKAKAK 723
                                         *******************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (721 nodes)
Target sequences:                          1  (726 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: 0.04u 0.02s 00:00:00.06 Elapsed: 00:00:00.05
# Mc/sec: 9.14
//
[ok]

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

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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