Alignments for a candidate for gcvT in Dechlorosoma suillum PS

GapMind for catabolism of small carbon sources

Alignments for a candidate for gcvT in Dechlorosoma suillum PS

Align aminomethyltransferase; EC 2.1.2.10 (characterized)
to candidate Dsui_2735 Dsui_2735 glycine cleavage system T protein

Query= CharProtDB::CH_000563
         (364 letters)



>FitnessBrowser__PS:Dsui_2735
          Length = 363

 Score =  375 bits (963), Expect = e-108
 Identities = 202/372 (54%), Positives = 259/372 (69%), Gaps = 17/372 (4%)

Query: 1   MAQQTPLYEQHTLCGARMVDFHGWMMPLHYGSQIDEHHAVRTDAGMFDVSHMTIVDLRGS 60
           M +QT L + H    ARMVDF GW MP++YGSQI+EHHAVR D GMFDVSHM  VD+ G+
Sbjct: 1   MTKQTVLNKAHRALNARMVDFGGWDMPVNYGSQIEEHHAVRNDCGMFDVSHMCAVDVTGA 60

Query: 61  RTREFLRYLLANDVAKLTKSGKALYSGMLNASGGVIDDLIVYYFTEDFFRLVVNSATREK 120
             + FL  L+AN+V KL   GKALYS MLN +GGV+DDLIVYY T+  +R+V+N+ T +K
Sbjct: 61  DAKAFLLRLIANNVDKLKVPGKALYSAMLNEAGGVVDDLIVYYLTDTHYRVVINAGTADK 120

Query: 121 DLSWITQHAEPFGIEITV------RDDLSMIAVQGPNAQAKAATLFNDAQRQAVEGMKPF 174
           DL+W+ Q    + ++++V         ++MIAVQGP A+AK   +  +  + A + + PF
Sbjct: 121 DLAWMDQLLGQWQLDVSVIPLREGPKAVAMIAVQGPQAKAKVWQVLPEV-KAATKNLAPF 179

Query: 175 FGVQAGDLFIATTGYTGEAGYEIALPNEKAADFWRALVEAGVKPCGLGARDTLRLEAGMN 234
           FG Q G  FIATTGYTGE G+EIALP  KA DFW AL+ AGV+PCGLGARDTLRLEAGMN
Sbjct: 180 FGTQIGQFFIATTGYTGEDGFEIALPAAKAEDFWNALIAAGVRPCGLGARDTLRLEAGMN 239

Query: 235 LYGQEMDETISPLAANMGWTIAWEPADRDFIGREALEVQREHGTEKLVGLVMTEKGVLRN 294
           LYGQ+MDET+SPL A + WT+  + ++RDF+G+ AL    +    + +GL + +KGVLR 
Sbjct: 240 LYGQDMDETVSPLDAGLAWTVDLK-SERDFVGKSALLANGQKA--QFLGLKLLDKGVLRA 296

Query: 295 ELPVRFTDAQGNQHEGIITSGTFSPTLGYSIALARVPEG--IGETAIVQIRNREMPVKVT 352
              V       +Q EG ITSGTFSPTL  SIALAR+P G  IG+T  V IR + +  +V 
Sbjct: 297 HQKV-----VTSQGEGEITSGTFSPTLEQSIALARLPLGVAIGDTVQVDIRGKLLNAQVV 351

Query: 353 KPVFVRNGKAVA 364
           KPVF R+GKAVA
Sbjct: 352 KPVFARHGKAVA 363


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: 441
Number of extensions: 28
Number of successful extensions: 6
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: 363
Length adjustment: 29
Effective length of query: 335
Effective length of database: 334
Effective search space:   111890
Effective search space used:   111890
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 Dsui_2735 Dsui_2735 (glycine cleavage system T protein)
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.24505.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   8.5e-128  412.2   0.1   9.7e-128  412.0   0.1    1.0  1  lcl|FitnessBrowser__PS:Dsui_2735  Dsui_2735 glycine cleavage syste


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PS:Dsui_2735  Dsui_2735 glycine cleavage system T protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  412.0   0.1  9.7e-128  9.7e-128       2     361 ..       3     357 ..       2     358 .. 0.92

  Alignments for each domain:
  == domain 1  score: 412.0 bits;  conditional E-value: 9.7e-128
                         TIGR00528   2 krtpLydlhtelggklvdfaGwelPvqykslieeheavrtkaGlfDvshmgkvelsGskslkfLqrllanDvdaLtk 78 
                                       k+t L + h  l +++vdf+Gw +Pv+y+s+ieeh+avr++ G+fDvshm  v+++G ++ +fL rl+an+vd+L +
  lcl|FitnessBrowser__PS:Dsui_2735   3 KQTVLNKAHRALNARMVDFGGWDMPVNYGSQIEEHHAVRNDCGMFDVSHMCAVDVTGADAKAFLLRLIANNVDKLKV 79 
                                       89*************************************************************************98 PP

                         TIGR00528  79 .GkaqysvllnaqGGvvDDlivykegednrfllvvnaataekDlewlkehlee...evtldtls...keisllalqG 148
                                        Gka+ys++ln  GGvvDDlivy+ ++  ++++v+na+ta+kDl+w+ + l +   +v+++ l+   k ++++a+qG
  lcl|FitnessBrowser__PS:Dsui_2735  80 pGKALYSAMLNEAGGVVDDLIVYYLTDT-HYRVVINAGTADKDLAWMDQLLGQwqlDVSVIPLRegpKAVAMIAVQG 155
                                       8*************************99.******************98764321144444444222667******* PP

                         TIGR00528 149 Pkakt.iledl..ldkaveglkefffvqeaelalkkaliartGytGedGfeiavanekavelwkklveaygvkPiGL 222
                                       P+ak+ + + l  +++a ++l +ff+ q +++     +ia+tGytGedGfeia++  ka ++w++l++a gv+P+GL
  lcl|FitnessBrowser__PS:Dsui_2735 156 PQAKAkVWQVLpeVKAATKNLAPFFGTQIGQF-----FIATTGYTGEDGFEIALPAAKAEDFWNALIAA-GVRPCGL 226
                                       *9986354543225667788************.....********************************.******* PP

                         TIGR00528 223 garDtLrleagmaLyGqeldeeitPleaglgwvvkkerkksdfiGravleeqkengtekklvGlemlekgiarnelk 299
                                       garDtLrleagm+LyGq++de+++Pl+agl w+v ++ +++df+G+++l    +ng + +  Gl++l+kg++r + k
  lcl|FitnessBrowser__PS:Dsui_2735 227 GARDTLRLEAGMNLYGQDMDETVSPLDAGLAWTVDLK-SERDFVGKSAL---LANGQKAQFLGLKLLDKGVLRAHQK 299
                                       *************************************.*********99...57999999***************** PP

                         TIGR00528 300 vlltngekevGivtsGtlsPtLgknialayvdkelekiGtklevevrnklvkikvvkklfvr 361
                                       v++++g   +G +tsGt+sPtL+++iala+++ ++  iG++++v++r+kl++++vvk++f r
  lcl|FitnessBrowser__PS:Dsui_2735 300 VVTSQG---EGEITSGTFSPTLEQSIALARLPLGV-AIGDTVQVDIRGKLLNAQVVKPVFAR 357
                                       ***888...9**********************776.6**********************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (362 nodes)
Target sequences:                          1  (363 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: 10.08
//
[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