Alignments for a candidate for glcB in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Alignments for a candidate for glcB in Dinoroseobacter shibae DFL-12

Align Malate synthase G (EC 2.3.3.9) (characterized)
to candidate 3607819 Dshi_1227 malate synthase G (RefSeq)

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



>FitnessBrowser__Dino:3607819
          Length = 724

 Score =  874 bits (2258), Expect = 0.0
 Identities = 439/722 (60%), Positives = 549/722 (76%), Gaps = 11/722 (1%)

Query: 3   ERVQVGGLQVAKVLYDFVNNEAIPGTGVDAAAFWAGADSVIHDLAPKNRALLAKRDDLQA 62
           +RV+  GLQVA  L +F+  +A+PGTGV AAAFW G  +++H+  P NRALLAKR +LQ 
Sbjct: 2   KRVERAGLQVAPELVEFLETQALPGTGVTAAAFWEGLSALVHEEGPTNRALLAKRTELQR 61

Query: 63  QIDAWHQARAGQAHDAVAYKSFLQEIGYLLPEAEDFQATTENVDEEIARMAGPQLVVPIM 122
           +IDAWH AR GQ HDA AY +FL+EIGYL+PE EDF+  T NVD EIA + GPQLVVPI 
Sbjct: 62  KIDAWHVARKGQPHDAAAYAAFLREIGYLVPEPEDFEIDTANVDPEIATIPGPQLVVPIT 121

Query: 123 NARFALNAANARWGSLYDALYGTDAISEADGASKGPGYNEIRGNKVIAYARNFLNEAAPL 182
           NAR+ALNAANARWGSLYDALYGTDA+ +      G G++  RG +V+A+AR+ L+ AAP+
Sbjct: 122 NARYALNAANARWGSLYDALYGTDALGDLPS---GKGFDPERGARVMAWARDHLDHAAPI 178

Query: 183 ETGSHVDSTGYRIEGGKLVVSLKDGSTTGLKNPAQLQGFQ-GEASAPIAVLLKNNGIHFE 241
              S  D T   +  G L   L  G    L +PAQ  G+  G A    +VLL+ NG+H  
Sbjct: 179 AGVSWADVTRIDVADGAL--ELVAGDLRPLVDPAQFAGYTTGPAGDVTSVLLRKNGLHLR 236

Query: 242 IQIDPASPIGQTDAAGVKDILMESALTTIMDCEDSIAAVDADDKTVVYRNWLGLMKGDLV 301
           + IDP S IG  D AG+ D+++E+A++ IMDCEDS+AAVDA+DK + Y NWLGLMKGDL 
Sbjct: 237 VMIDPTSRIGAADPAGISDVIIEAAISAIMDCEDSVAAVDAEDKVLAYGNWLGLMKGDLS 296

Query: 302 EELEKGGKRITRAMNPDRVYTKADGNGELTLHGRSLLFIRNVGHLMTNDAILDKEGNEVP 361
           +E+ KGGK  TRA+  D V T  +G+  L L GR+L+ +RNVGHLMTN AILD++G E+ 
Sbjct: 297 QEVTKGGKSFTRALARDVVATAPNGD-RLVLKGRALMLVRNVGHLMTNPAILDRDGAEIG 355

Query: 362 EGIMDGLFTSLIAVHNLNGNTSRKNTRTGSMYIVKPKMHGPEEVAFATELFGRVEDVLGL 421
           EG+MD + T+LIA+H+L    +  N+  GS+Y+VKPKMHGPEEVAF   +F RVE  LGL
Sbjct: 356 EGLMDAMVTTLIAMHDLG--RAGGNSVHGSVYVVKPKMHGPEEVAFTDRIFTRVEAALGL 413

Query: 422 PRNTLKVGIMDEERRTTINLKACIKEARERVVFINTGFLDRTGDEIHTSMEAGPMVRKAA 481
           P NT+K+GIMDEERRT+ NLKACI  AR RV FINTGFLDRTGDEIHTSMEAGP++ K  
Sbjct: 414 PANTVKIGIMDEERRTSANLKACIHAARSRVAFINTGFLDRTGDEIHTSMEAGPVLPKGE 473

Query: 482 MKAEKWISAYENNNVDVGLACGLQGKAQIGKGMWAMPDLMAAMLEQKVGHPMAGANTAWV 541
           MK   WI+AYE+ NVD+GLACGL+G+AQIGKGMWAMPDLMA MLE K+GHPM+GAN AWV
Sbjct: 474 MKGTAWIAAYEDRNVDIGLACGLKGRAQIGKGMWAMPDLMADMLEAKIGHPMSGANCAWV 533

Query: 542 PSPTAATLHAMHYHKIDVQARQVELAK-REKASIDDILTIPLAQDTNWSEEEKRNELDNN 600
           PSPTAATLHA HYHK+DV ARQ E+A    + +++D+LTIPL +  + S  E   E++NN
Sbjct: 534 PSPTAATLHATHYHKVDVFARQDEIAAGGARGTLEDLLTIPLLEGRSLSAAEIAAEVENN 593

Query: 601 SQGILGYMVRWVEQGVGCSKVPDINDIALMEDRATLRISSQHVANWMRHGVVTKDQVVES 660
           +QGILGY+VRW++QGVGCSKVPDI+D+ LMEDRAT RISSQ +ANW+ HG+V+++QV+ +
Sbjct: 594 AQGILGYVVRWIDQGVGCSKVPDIHDVGLMEDRATCRISSQALANWLHHGIVSEEQVMGA 653

Query: 661 LKRMAPVVDRQNQGDPLYRPMAPDFDNSVAFQAALELVLEGTKQPNGYTEPVLHRRRREF 720
           L++MA VVD+QN GDP YRPMAP FD  +AF AA +LV  G +QP+GYTEPVLH RR E 
Sbjct: 654 LRKMAAVVDQQNAGDPAYRPMAPGFD-GIAFAAACDLVFAGREQPSGYTEPVLHARRLEL 712

Query: 721 KA 722
           KA
Sbjct: 713 KA 714


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: 1448
Number of extensions: 66
Number of successful extensions: 7
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: 724
Length adjustment: 40
Effective length of query: 686
Effective length of database: 684
Effective search space:   469224
Effective search space used:   469224
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 3607819 Dshi_1227 (malate synthase G (RefSeq))
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.8975.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 1073.9   0.0          0 1073.7   0.0    1.0  1  lcl|FitnessBrowser__Dino:3607819  Dshi_1227 malate synthase G (Ref


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dino:3607819  Dshi_1227 malate synthase G (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1073.7   0.0         0         0       2     719 ..       3     714 ..       2     716 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1073.7 bits;  conditional E-value: 0
                         TIGR01345   2 rvdagrlqvakklkdfveeevlpgtgvdaekfwsgfdeivrdlapenrellakrdeiqaaideyhrknk.gvidkea 77 
                                       rv+ ++lqva +l++f+e ++lpgtgv a++fw+g++++v++  p nr llakr e+q  id++h   k  + d +a
  lcl|FitnessBrowser__Dino:3607819   3 RVERAGLQVAPELVEFLETQALPGTGVTAAAFWEGLSALVHEEGPTNRALLAKRTELQRKIDAWHVARKgQPHDAAA 79 
                                       688999************************************************************9995689**** PP

                         TIGR01345  78 yksflkeigylveepervtietenvdseiasqagpqlvvpvlnaryalnaanarwgslydalygsnvipeedgaekg 154
                                       y  fl+eigylv+epe  +i+t nvd eia+  gpqlvvp++naryalnaanarwgslydalyg++++ +   + +g
  lcl|FitnessBrowser__Dino:3607819  80 YAAFLREIGYLVPEPEDFEIDTANVDPEIATIPGPQLVVPITNARYALNAANARWGSLYDALYGTDALGD---LPSG 153
                                       *******************************************************************976...6788 PP

                         TIGR01345 155 keynpkrgekviefarefldeslplesgsyadvvkykivdkklavqlesgkvtrlkdeeqfvgyr.gdaadpevill 230
                                       k ++p+rg +v+++ar+ ld++ p+ + s+adv + ++ d+ l   l +g+   l d++qf gy+ g a+d + +ll
  lcl|FitnessBrowser__Dino:3607819 154 KGFDPERGARVMAWARDHLDHAAPIAGVSWADVTRIDVADGALE--LVAGDLRPLVDPAQFAGYTtGPAGDVTSVLL 228
                                       89***************************************986..5567999***********64899******** PP

                         TIGR01345 231 ktnglhielqidarhpigkadkakvkdivlesaittildcedsvaavdaedkvlvyrnllglmkgtlkeklekngri 307
                                       ++nglh+ + id++ +ig ad+a++ d+++e+ai++i+dcedsvaavdaedkvl y n+lglmkg+l ++++k g+ 
  lcl|FitnessBrowser__Dino:3607819 229 RKNGLHLRVMIDPTSRIGAADPAGISDVIIEAAISAIMDCEDSVAAVDAEDKVLAYGNWLGLMKGDLSQEVTKGGKS 305
                                       ***************************************************************************** PP

                         TIGR01345 308 ikrklnedrsytaangeelslhgrsllfvrnvghlmtipviltdegeeipegildgvltsvialydlkvqnklrnsr 384
                                       ++r l  d + ta+ng+ l+l+gr+l++vrnvghlmt+p+il+ +g ei eg++d+++t++ia++dl + +   ns 
  lcl|FitnessBrowser__Dino:3607819 306 FTRALARDVVATAPNGDRLVLKGRALMLVRNVGHLMTNPAILDRDGAEIGEGLMDAMVTTLIAMHDLGRAG--GNSV 380
                                       ********************************************************************987..9*** PP

                         TIGR01345 385 kgsvyivkpkmhgpeevafanklftriedllglerhtlkvgvmdeerrtslnlkaciakvkervafintgfldrtgd 461
                                       +gsvy+vkpkmhgpeevaf++++ftr+e  lgl+ +t+k+g+mdeerrts nlkaci+ ++ rvafintgfldrtgd
  lcl|FitnessBrowser__Dino:3607819 381 HGSVYVVKPKMHGPEEVAFTDRIFTRVEAALGLPANTVKIGIMDEERRTSANLKACIHAARSRVAFINTGFLDRTGD 457
                                       ***************************************************************************** PP

                         TIGR01345 462 eihtsmeagamvrkadmksapwlkayernnvaagltcglrgkaqigkgmwampdlmaemlekkgdqlragantawvp 538
                                       eihtsmeag+++ k++mk ++w+ aye  nv+ gl cgl+g+aqigkgmwampdlma+mle k++ + +gan awvp
  lcl|FitnessBrowser__Dino:3607819 458 EIHTSMEAGPVLPKGEMKGTAWIAAYEDRNVDIGLACGLKGRAQIGKGMWAMPDLMADMLEAKIGHPMSGANCAWVP 534
                                       ***************************************************************************** PP

                         TIGR01345 539 sptaatlhalhyhrvdvqkvqkeladaerraelkeiltipvaentnwseeeikeeldnnvqgilgyvvrwveqgigc 615
                                       sptaatlha+hyh+vdv++ q+e+a+ + r +l+++ltip+ e    s+ ei +e++nn+qgilgyvvrw++qg+gc
  lcl|FitnessBrowser__Dino:3607819 535 SPTAATLHATHYHKVDVFARQDEIAAGGARGTLEDLLTIPLLEGRSLSAAEIAAEVENNAQGILGYVVRWIDQGVGC 611
                                       ***************************************************************************** PP

                         TIGR01345 616 skvpdihnvalmedratlrissqhlanwlrhgivskeqvleslermakvvdkqnagdeayrpmadnleasvafkaak 692
                                       skvpdih+v lmedrat rissq lanwl hgivs eqv+ +l +ma vvd+qnagd+ayrpma+ ++  +af aa 
  lcl|FitnessBrowser__Dino:3607819 612 SKVPDIHDVGLMEDRATCRISSQALANWLHHGIVSEEQVMGALRKMAAVVDQQNAGDPAYRPMAPGFD-GIAFAAAC 687
                                       *******************************************************************8.69****** PP

                         TIGR01345 693 dlilkgtkqpsgytepilharrlefke 719
                                       dl++ g +qpsgytep+lharrle k+
  lcl|FitnessBrowser__Dino:3607819 688 DLVFAGREQPSGYTEPVLHARRLELKA 714
                                       ************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (721 nodes)
Target sequences:                          1  (724 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: 12.25
//
[ok]

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

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Protein sequences (fasta format)
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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