Alignments for a candidate for glcB in Sulfuritalea hydrogenivorans sk43H DSM 22779

GapMind for catabolism of small carbon sources

Alignments for a candidate for glcB in Sulfuritalea hydrogenivorans sk43H DSM 22779

Align Malate synthase (EC 2.3.3.9) (characterized)
to candidate WP_041097653.1 SUTH_RS05370 malate synthase A

Query= reanno::BFirm:BPHYT_RS12305
         (536 letters)



>NCBI__GCF_000828635.1:WP_041097653.1
          Length = 530

 Score =  772 bits (1994), Expect = 0.0
 Identities = 374/528 (70%), Positives = 440/528 (83%), Gaps = 5/528 (0%)

Query: 11  LQLPQGMEITAEIKPGYDAILSREALELVAALHRTFEPRRQQLLQARAERTKRLDAGERP 70
           + LP G++I A I   Y  IL+ EA+ LVA LHR FEPRRQ+LL+AR  R  R+DAGE P
Sbjct: 1   MSLPAGVQINAPITADYAKILTPEAMALVAKLHRAFEPRRQELLKARVARQARIDAGEMP 60

Query: 71  DFLAETKSVRDGDWTIAPLPQDLQCRRVEITGPVERKMIINALNSGADSYMTDFEDSNAP 130
           DFL ETKS+R+GDW IAPLP+ L+ RR EITGPVE KMIINA NSGADSYMTDFEDSN+P
Sbjct: 61  DFLPETKSIREGDWKIAPLPKALERRRTEITGPVEAKMIINAYNSGADSYMTDFEDSNSP 120

Query: 131 SWDNQITGHINLKDAVRRTISLEQN-GKSYTLNDKVATLIVRPRGWHLDEKHVKVDGKRV 189
            WDNQI G +NL  A+RR +S +   GK Y LNDK+ATL VRPRGWHLDEKHV +DG+RV
Sbjct: 121 KWDNQIQGQVNLYKAIRRELSFKNEAGKEYKLNDKIATLQVRPRGWHLDEKHVLIDGQRV 180

Query: 190 SGGIFDFALFMVHNAKELVARGSGPYFYLPKMESHLEARLWNDIFVAAQEAVGVPRGTIR 249
           SGG+FDFALF+ HNAKE +ARG+GP+FYLPKMESHLEARLWNDIFV AQ  +G+P+GTI+
Sbjct: 181 SGGVFDFALFLFHNAKEQIARGAGPFFYLPKMESHLEARLWNDIFVMAQNEIGLPQGTIK 240

Query: 250 ATVLIETIVAAFEMDEILYELREHSSGLNAGRWDYIFSAIKKFKADRDFCLADRSQITMT 309
           ATVLIETI+A FE++EILYELR+HS+GLNAGRWDYIFS IKKFK ++DFCLA+R  ITM 
Sbjct: 241 ATVLIETILATFELEEILYELRQHSAGLNAGRWDYIFSCIKKFKRNKDFCLANRGAITME 300

Query: 310 SPFMRAYALLLLKTCHRRNAPAIGGMSALIPIKNDPAANDKAMSGVRSDKARDAGDGYDG 369
            PFMR+YAL L+K CH+R APAIGGMSALIPIKNDP AN+KA++G+R DK RDA DG+DG
Sbjct: 301 VPFMRSYALSLVKACHKRGAPAIGGMSALIPIKNDPVANEKALAGIRHDKTRDANDGFDG 360

Query: 370 GWVAHPGLVPIAMEEFVKVLGDKPNQIGKQRDDVLVTATDLTDFRPEAPITEGGLRNNIN 429
           GWVAHPGLVPIA EEF KVLG++PNQ  KQRD+      D  +F+PE PITE G+RNNIN
Sbjct: 361 GWVAHPGLVPIAAEEFQKVLGERPNQWEKQRDENF-GPKDWLNFQPEQPITEAGVRNNIN 419

Query: 430 VGIHYLGAWLAGNGCVPIHNLMEDAATAEISRSQVWQWIRSPKGKLEDGRKVTAELVREL 489
           VGIHYLG+WLAGNGCVPIHNLMEDAATAEISRSQVWQW+ SPKGKL+DGRKVTA++VR +
Sbjct: 420 VGIHYLGSWLAGNGCVPIHNLMEDAATAEISRSQVWQWVVSPKGKLDDGRKVTADMVRAI 479

Query: 490 SAQELEKVKQAV---GGDTKPYERAAQIFEEMSTSEQFTDFLTLPLYE 534
             +EL KVK  V   G  T+ Y++AA+IFEEMS ++ + +FLTLPLYE
Sbjct: 480 IPEELAKVKATVTAQGEKTETYDQAAKIFEEMSLADSYPEFLTLPLYE 527


Lambda     K      H
   0.318    0.134    0.397 

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: 818
Number of extensions: 18
Number of successful extensions: 5
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: 536
Length of database: 530
Length adjustment: 35
Effective length of query: 501
Effective length of database: 495
Effective search space:   247995
Effective search space used:   247995
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 (21.7 bits)
S2: 52 (24.6 bits)

Align candidate WP_041097653.1 SUTH_RS05370 (malate synthase A)
to HMM TIGR01344 (aceB: malate synthase A (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/TIGR01344.hmm
# target sequence database:        /tmp/gapView.659211.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01344  [M=511]
Accession:   TIGR01344
Description: malate_syn_A: malate synthase A
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     2e-227  741.4   0.0   2.3e-227  741.2   0.0    1.0  1  NCBI__GCF_000828635.1:WP_041097653.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000828635.1:WP_041097653.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  741.2   0.0  2.3e-227  2.3e-227       1     510 [.      20     529 ..      20     530 .] 0.98

  Alignments for each domain:
  == domain 1  score: 741.2 bits;  conditional E-value: 2.3e-227
                             TIGR01344   1 vltkealeflaelhrrfaerrkellarrekkqakldkgelldflpetkeireddwkvaaipadlldrrveitG 73 
                                           +lt+ea++++a+lhr f++rr+ell++r ++qa++d+ge++dflpetk+ire+dwk+a++p++l  rr+eitG
  NCBI__GCF_000828635.1:WP_041097653.1  20 ILTPEAMALVAKLHRAFEPRRQELLKARVARQARIDAGEMPDFLPETKSIREGDWKIAPLPKALERRRTEITG 92 
                                           89*********************************************************************** PP

                             TIGR01344  74 PvdrkmvinalnaeakvfladfedsssPtwenvveGqinlkdairgeidftdeesgkeyalkaklavlivrpr 146
                                           Pv+ km+ina n++a  +++dfeds+sP w+n ++Gq+nl+ air+e++f++ e+gkey+l+ k a+l vrpr
  NCBI__GCF_000828635.1:WP_041097653.1  93 PVEAKMIINAYNSGADSYMTDFEDSNSPKWDNQIQGQVNLYKAIRRELSFKN-EAGKEYKLNDKIATLQVRPR 164
                                           ***************************************************7.99****************** PP

                             TIGR01344 147 GwhlkerhleidgkaisgslldfglyffhnarellkkGkGPyfylPkleshlearlwndvfllaqevlglprG 219
                                           Gwhl e+h+ idg+ +sg ++df+l++fhna+e++++G GP+fylPk+eshlearlwnd+f++aq+++glp+G
  NCBI__GCF_000828635.1:WP_041097653.1 165 GWHLDEKHVLIDGQRVSGGVFDFALFLFHNAKEQIARGAGPFFYLPKMESHLEARLWNDIFVMAQNEIGLPQG 237
                                           ************************************************************************* PP

                             TIGR01344 220 tikatvlietlpaafemdeilyelrehssGlncGrwdyifslikklkkaeevvlPdrdavtmdkaflnayskl 292
                                           tikatvliet+ a+fe++eilyelr+hs+Gln+Grwdyifs+ikk+k+++++ l +r a+tm+ +f+++y+  
  NCBI__GCF_000828635.1:WP_041097653.1 238 TIKATVLIETILATFELEEILYELRQHSAGLNAGRWDYIFSCIKKFKRNKDFCLANRGAITMEVPFMRSYALS 310
                                           ************************************************************************* PP

                             TIGR01344 293 liqtchrrgafalGGmaafiPikddpaaneaalekvradkereaknGhdGtwvahPdlvevalevfdevlge. 364
                                           l+++ch+rga a+GGm+a iPik+dp ane+al+ +r dk+r+a++G+dG wvahP+lv++a e f++vlge 
  NCBI__GCF_000828635.1:WP_041097653.1 311 LVKACHKRGAPAIGGMSALIPIKNDPVANEKALAGIRHDKTRDANDGFDGGWVAHPGLVPIAAEEFQKVLGEr 383
                                           ************************************************************************9 PP

                             TIGR01344 365 pnqldrvrledvsitaaellev.kdasrteeGlrenirvglryieawlrGsGavpiynlmedaataeisraql 436
                                           pnq +++r+   + +  + l+  ++   te+G+r+ni+vg++y+ +wl G+G+vpi+nlmedaataeisr+q+
  NCBI__GCF_000828635.1:WP_041097653.1 384 PNQWEKQRD--ENFGPKDWLNFqPEQPITEAGVRNNINVGIHYLGSWLAGNGCVPIHNLMEDAATAEISRSQV 454
                                           *****9995..55679999999678889********************************************* PP

                             TIGR01344 437 wqwikhGv.vledGekvtselvrdllkeeleklkkesgkeeyakarleeaaellerlvlseeledfltlpayd 508
                                           wqw+   +  l+dG+kvt+++vr ++ eel+k+k +++ +   ++ +++aa+++e+++l++++++fltlp+y+
  NCBI__GCF_000828635.1:WP_041097653.1 455 WQWVVSPKgKLDDGRKVTADMVRAIIPEELAKVKATVTAQGEKTETYDQAAKIFEEMSLADSYPEFLTLPLYE 527
                                           ***9876537**************************998888999**************************** PP

                             TIGR01344 509 el 510
                                           ++
  NCBI__GCF_000828635.1:WP_041097653.1 528 AM 529
                                           87 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (511 nodes)
Target sequences:                          1  (530 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 13.57
//
[ok]

This GapMind analysis is from Apr 09 2024. 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 2024 update 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