Alignments for a candidate for gcvT in Desulfitobacterium hafniense DCB-2

GapMind for catabolism of small carbon sources

Alignments for a candidate for gcvT in Desulfitobacterium hafniense DCB-2

Align aminomethyltransferase; EC 2.1.2.10 (characterized)
to candidate WP_005811336.1 DHAF_RS20145 aminomethyltransferase

Query= CharProtDB::CH_000563
         (364 letters)



>NCBI__GCF_000021925.1:WP_005811336.1
          Length = 365

 Score =  266 bits (679), Expect = 9e-76
 Identities = 155/365 (42%), Positives = 221/365 (60%), Gaps = 16/365 (4%)

Query: 3   QQTPLYEQHTLCGARMVDFHGWMMPLHYGSQIDEHHAVRTDAGMFDVSHMTIVDLRGSRT 62
           ++TPLYEQH   GA+++DF GW MP+ Y   I+EH AVR+ AG+FDVSHM  V+L+G  +
Sbjct: 5   KRTPLYEQHRRAGAKLIDFGGWEMPVQYAGVIEEHKAVRSKAGLFDVSHMGEVELKGKDS 64

Query: 63  REFLRYLLANDVAKLTKSGKALYSGMLNASGGVIDDLIVYYFTEDFFRLVVNSATREKDL 122
             FL+YLL NDV+++ +  +  YS M  ++GGV+DDL+VY ++ + F LVVN++  +KD 
Sbjct: 65  LAFLQYLLTNDVSRI-QDNQIQYSPMCTSAGGVVDDLLVYRYSREHFLLVVNASNTDKDF 123

Query: 123 SWITQHAEPFGIEITVRD-DLSMIAVQGPNAQAKAATLFNDAQRQAVEGMKPFFGVQAGD 181
           +W+   AE F I +  R  D + +A+QGP A+     L +    Q          V    
Sbjct: 124 AWMQAQAEGFEISLENRSGDFAQLALQGPWAEKILQKLTSMDLAQINYYWFKHGEVDGVL 183

Query: 182 LFIATTGYTGEAGYEIALPNEKAADFWRALVEA----GVKPCGLGARDTLRLEAGMNLYG 237
             I+ TGYTGE G+EI LP E A   W  ++E     GV+P GLGARDTLR EA + LYG
Sbjct: 184 CLISRTGYTGEDGFEIYLPPEHAPRMWERILEVGGSEGVQPIGLGARDTLRFEARLPLYG 243

Query: 238 QEMDETISPLAANMGWTIAWEPADRDFIGREALEVQREHGT-EKLVGLVMTEKGVLRNEL 296
            E+   I+PL A +G+ +  E    +FIG+EAL  Q+E G   KLVGL M E+G+ R+  
Sbjct: 244 NELGPDITPLEAGLGFFVKLE--KDNFIGKEALSAQKEKGVPRKLVGLEMIERGIARSHY 301

Query: 297 PVRFTDAQGNQHEGIITSGTFSPTLGYSIALARVP---EGIGETAIVQIRNREMPVKVTK 353
           P++    +  +  G ITSG+FSPTL  +IAL  +P     IGET  V IR + +  ++  
Sbjct: 302 PLQ----KEGKEIGFITSGSFSPTLNKNIALGLIPPEYAQIGETLDVIIRGKAVKARIIP 357

Query: 354 PVFVR 358
            +F +
Sbjct: 358 SLFYK 362


Lambda     K      H
   0.320    0.136    0.402 

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: 394
Number of extensions: 24
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: 364
Length of database: 365
Length adjustment: 29
Effective length of query: 335
Effective length of database: 336
Effective search space:   112560
Effective search space used:   112560
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 bits)

Align candidate WP_005811336.1 DHAF_RS20145 (aminomethyltransferase)
to HMM TIGR00528 (gcvT: glycine cleavage system T protein (EC 2.1.2.10))

# 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/TIGR00528.hmm
# target sequence database:        /tmp/gapView.9877.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00528  [M=362]
Accession:   TIGR00528
Description: gcvT: glycine cleavage system T protein
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   9.4e-138  445.0   0.0   1.1e-137  444.8   0.0    1.0  1  lcl|NCBI__GCF_000021925.1:WP_005811336.1  DHAF_RS20145 aminomethyltransfer


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000021925.1:WP_005811336.1  DHAF_RS20145 aminomethyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  444.8   0.0  1.1e-137  1.1e-137       1     362 []       4     363 ..       4     363 .. 0.98

  Alignments for each domain:
  == domain 1  score: 444.8 bits;  conditional E-value: 1.1e-137
                                 TIGR00528   1 lkrtpLydlhtelggklvdfaGwelPvqykslieeheavrtkaGlfDvshmgkvelsGskslkfLqrll 69 
                                               lkrtpLy++h   g+kl+df+Gwe+Pvqy+++ieeh+avr kaGlfDvshmg+vel+G++sl+fLq+ll
  lcl|NCBI__GCF_000021925.1:WP_005811336.1   4 LKRTPLYEQHRRAGAKLIDFGGWEMPVQYAGVIEEHKAVRSKAGLFDVSHMGEVELKGKDSLAFLQYLL 72 
                                               69******************************************************************* PP

                                 TIGR00528  70 anDvdaLtkGkaqysvllnaqGGvvDDlivykegednrfllvvnaataekDlewlkehlee.evtldtl 137
                                               +nDv+++   + qys ++ + GGvvDDl+vy+ + + +fllvvna++++kD +w++ ++e+ e++l++ 
  lcl|NCBI__GCF_000021925.1:WP_005811336.1  73 TNDVSRIQDNQIQYSPMCTSAGGVVDDLLVYRYSRE-HFLLVVNASNTDKDFAWMQAQAEGfEISLENR 140
                                               **********************************99.9*********************9935789999 PP

                                 TIGR00528 138 skeisllalqGPkaktiledlldkaveglkefffvqeaelalkkaliartGytGedGfeiavanekave 206
                                               s + + lalqGP a++il++l++ ++ +++ + f  ++e+ +  +li+rtGytGedGfei++++e+a  
  lcl|NCBI__GCF_000021925.1:WP_005811336.1 141 SGDFAQLALQGPWAEKILQKLTSMDLAQINYYWFK-HGEVDGVLCLISRTGYTGEDGFEIYLPPEHAPR 208
                                               *****************************998887.99**99999************************ PP

                                 TIGR00528 207 lwkklvea...ygvkPiGLgarDtLrleagmaLyGqeldeeitPleaglgwvvkkerkksdfiGravle 272
                                               +w++++e     gv+PiGLgarDtLr+ea ++LyG+el  +itPleaglg+ vk+e  k +fiG+++l+
  lcl|NCBI__GCF_000021925.1:WP_005811336.1 209 MWERILEVggsEGVQPIGLGARDTLRFEARLPLYGNELGPDITPLEAGLGFFVKLE--KDNFIGKEALS 275
                                               ******987779*******************************************9..899******** PP

                                 TIGR00528 273 eqkengtekklvGlemlekgiarnelkvlltngekevGivtsGtlsPtLgknialayvdkelekiGtkl 341
                                                qke+g+ +klvGlem+e+giar ++++ + +g ke+G +tsG++sPtL+knial++++ e+++iG++l
  lcl|NCBI__GCF_000021925.1:WP_005811336.1 276 AQKEKGVPRKLVGLEMIERGIARSHYPLQK-EG-KEIGFITSGSFSPTLNKNIALGLIPPEYAQIGETL 342
                                               ***************************999.99.9********************************** PP

                                 TIGR00528 342 evevrnklvkikvvkklfvrs 362
                                               +v +r+k vk++++  lf+++
  lcl|NCBI__GCF_000021925.1:WP_005811336.1 343 DVIIRGKAVKARIIPSLFYKR 363
                                               ******************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (362 nodes)
Target sequences:                          1  (365 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: 8.98
//
[ok]

This GapMind analysis is from Sep 24 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