Alignments for a candidate for gcvT in Shewanella loihica PV-4

GapMind for catabolism of small carbon sources

Alignments for a candidate for gcvT in Shewanella loihica PV-4

Align Aminomethyltransferase (EC 2.1.2.10) (characterized)
to candidate 5210636 Shew_3064 glycine cleavage system aminomethyltransferase T (RefSeq)

Query= reanno::Koxy:BWI76_RS23880
         (364 letters)



>FitnessBrowser__PV4:5210636
          Length = 364

 Score =  514 bits (1323), Expect = e-150
 Identities = 251/361 (69%), Positives = 294/361 (81%)

Query: 1   MAQQTPLFEQHTLCGARMVDFHGWMMPLHYGSQIDEHHAVRGDAGMFDVSHMTIVDFHGS 60
           MA +T LF +H    A+MVDFHGW MPL+YGSQI+EHH VR DAGMFDVSHMT+VD  G+
Sbjct: 1   MANKTVLFNKHLEANAKMVDFHGWDMPLNYGSQIEEHHVVRQDAGMFDVSHMTVVDVTGA 60

Query: 61  RIREFLRYLLANDVAKLTVPGKALYSGMLTASGGVIDDLIVYFLSEDYFRLVVNSATREK 120
              +FLR LLANDVAKL VPGKALY GML  + GVIDDLI Y+LS+ ++R+VVNSATREK
Sbjct: 61  EACDFLRKLLANDVAKLKVPGKALYGGMLDHNAGVIDDLITYYLSDTHYRIVVNSATREK 120

Query: 121 DLAWIAQQSESYGLEITVRDDLSLIAVQGPRAKEKAATLFTDAQRQAVEGMKPFFGVQAG 180
           DLAWI +Q + Y + +T R +L++IAVQGP AK KAA +FTD Q  AVEGMKPFFGVQ+G
Sbjct: 121 DLAWITEQVKGYDVTVTERPELAMIAVQGPNAKAKAAAVFTDEQNAAVEGMKPFFGVQSG 180

Query: 181 DLFIATTGYTGEAGYEIALPNEQAVDFWRGLLDAGVKPCGLGARDTLRLEAGMNLYGQEM 240
            LFIATTGYTGEAGYEI +P  +A   W+ LLD GVKPCGLGARDTLRLEAGMNLYGQ+M
Sbjct: 181 SLFIATTGYTGEAGYEIIVPEAEAEALWQALLDNGVKPCGLGARDTLRLEAGMNLYGQDM 240

Query: 241 DEGVSPLAANMGWTIAWEPTDRDFIGREALEMQREKGTEQLVGLVMTEKGVLRGGLPVRF 300
           DE V+PLAANMGWTIAWEP DRDFIGREAL   +  GT++LVGLVM  KGVLR G+PV F
Sbjct: 241 DESVNPLAANMGWTIAWEPEDRDFIGREALAAIKAAGTDKLVGLVMEAKGVLRTGMPVFF 300

Query: 301 SDADGNQKEGIITSGTFSPTLGYSIALARVPEGIGETAVVQIRNREMPVKVTKPVFVRNG 360
           +DADG +++G ITSGTFSPTLGYSIA+ARVP  +G+ A V++R + +PVKV  P FVRNG
Sbjct: 301 TDADGVEQQGAITSGTFSPTLGYSIAMARVPNSVGDVAEVEMRKKRVPVKVIAPSFVRNG 360

Query: 361 K 361
           K
Sbjct: 361 K 361


Lambda     K      H
   0.320    0.137    0.407 

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: 502
Number of extensions: 13
Number of successful extensions: 1
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: 364
Length adjustment: 29
Effective length of query: 335
Effective length of database: 335
Effective search space:   112225
Effective search space used:   112225
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 5210636 Shew_3064 (glycine cleavage system aminomethyltransferase T (RefSeq))
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.12173.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
   3.2e-142  459.7   0.1   3.6e-142  459.5   0.1    1.0  1  lcl|FitnessBrowser__PV4:5210636  Shew_3064 glycine cleavage syste


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5210636  Shew_3064 glycine cleavage system aminomethyltransferase T (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  459.5   0.1  3.6e-142  3.6e-142       2     362 .]       3     359 ..       2     359 .. 0.98

  Alignments for each domain:
  == domain 1  score: 459.5 bits;  conditional E-value: 3.6e-142
                        TIGR00528   2 krtpLydlhtelggklvdfaGwelPvqykslieeheavrtkaGlfDvshmgkvelsGskslkfLqrllanDvdaLtk. 78 
                                      ++t L++ h e  +k+vdf+Gw +P++y+s+ieeh+ vr++aG+fDvshm+ v+++G ++ +fL++llanDv++L + 
  lcl|FitnessBrowser__PV4:5210636   3 NKTVLFNKHLEANAKMVDFHGWDMPLNYGSQIEEHHVVRQDAGMFDVSHMTVVDVTGAEACDFLRKLLANDVAKLKVp 80 
                                      79*************************************************************************988 PP

                        TIGR00528  79 GkaqysvllnaqGGvvDDlivykegednrfllvvnaataekDlewlkehleeevtldtlskeisllalqGP....kak 152
                                      Gka+y ++l  + Gv+DDli y+ ++  ++++vvn+at+ekDl+w++e++++     t + e++++a+qGP    ka+
  lcl|FitnessBrowser__PV4:5210636  81 GKALYGGMLDHNAGVIDDLITYYLSDT-HYRIVVNSATREKDLAWITEQVKGYDVTVTERPELAMIAVQGPnakaKAA 157
                                      ************************999.*******************************************9999999 PP

                        TIGR00528 153 tiledlldkaveglkefffvqeaelalkkaliartGytGedGfeiavanekavelwkklveaygvkPiGLgarDtLrl 230
                                      +++ d +++aveg+k+ff+vq + l     +ia+tGytGe+G+ei+v++ +a  lw++l+++ gvkP+GLgarDtLrl
  lcl|FitnessBrowser__PV4:5210636 158 AVFTDEQNAAVEGMKPFFGVQSGSL-----FIATTGYTGEAGYEIIVPEAEAEALWQALLDN-GVKPCGLGARDTLRL 229
                                      *************************.....********************************.*************** PP

                        TIGR00528 231 eagmaLyGqeldeeitPleaglgwvvkkerkksdfiGravleeqkengtekklvGlemlekgiarnelkvllt..nge 306
                                      eagm+LyGq++de++ Pl+a++gw++++e++++dfiGr++l   k+ gt+k lvGl+m +kg++r +++v++t  +g 
  lcl|FitnessBrowser__PV4:5210636 230 EAGMNLYGQDMDESVNPLAANMGWTIAWEPEDRDFIGREALAAIKAAGTDK-LVGLVMEAKGVLRTGMPVFFTdaDGV 306
                                      *************************************************99.********************966677 PP

                        TIGR00528 307 kevGivtsGtlsPtLgknialayvdkelekiGtklevevrnklvkikvvkklfvrs 362
                                      ++ G +tsGt+sPtLg++ia+a+v+   + +G+++eve+r+k v++kv+ + fvr+
  lcl|FitnessBrowser__PV4:5210636 307 EQQGAITSGTFSPTLGYSIAMARVP---NSVGDVAEVEMRKKRVPVKVIAPSFVRN 359
                                      99***********************...99***********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (362 nodes)
Target sequences:                          1  (364 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 11.88
//
[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