GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gcvT in Shewanella amazonensis SB2B

Align aminomethyltransferase; EC 2.1.2.10 (characterized)
to candidate 6938618 Sama_2721 glycine cleavage system aminomethyltransferase T (RefSeq)

Query= CharProtDB::CH_000563
         (364 letters)



>lcl|FitnessBrowser__SB2B:6938618 Sama_2721 glycine cleavage system
           aminomethyltransferase T (RefSeq)
          Length = 364

 Score =  521 bits (1342), Expect = e-152
 Identities = 254/361 (70%), Positives = 301/361 (83%)

Query: 1   MAQQTPLYEQHTLCGARMVDFHGWMMPLHYGSQIDEHHAVRTDAGMFDVSHMTIVDLRGS 60
           MA +T L+ +H    A+MVDFHGW MPL+YGSQI+EHHAVR DAGMFDVSHMT+VD+ G+
Sbjct: 1   MANKTVLFSKHLESNAKMVDFHGWNMPLNYGSQIEEHHAVRRDAGMFDVSHMTVVDVEGA 60

Query: 61  RTREFLRYLLANDVAKLTKSGKALYSGMLNASGGVIDDLIVYYFTEDFFRLVVNSATREK 120
             R FLR LLAND+AKLT  GKALY GMLN  GGVIDDLI YY ++  +R+VVNSATREK
Sbjct: 61  DARAFLRKLLANDIAKLTVPGKALYGGMLNHDGGVIDDLITYYLSDTQYRVVVNSATREK 120

Query: 121 DLSWITQHAEPFGIEITVRDDLSMIAVQGPNAQAKAATLFNDAQRQAVEGMKPFFGVQAG 180
           DL+WI + A+ F + IT R +L+MIAVQGPNA+AKAAT+F   Q  AVEGMKPFFG QAG
Sbjct: 121 DLAWIGEQAKGFDVTITERPELAMIAVQGPNAKAKAATVFTAEQNAAVEGMKPFFGKQAG 180

Query: 181 DLFIATTGYTGEAGYEIALPNEKAADFWRALVEAGVKPCGLGARDTLRLEAGMNLYGQEM 240
            LFIATTGYTGEAGYEI +P  +A   W+AL++AGV+PCGLGARDTLRLEAGMNLYGQ+M
Sbjct: 181 SLFIATTGYTGEAGYEIIVPEAEAEALWQALLDAGVQPCGLGARDTLRLEAGMNLYGQDM 240

Query: 241 DETISPLAANMGWTIAWEPADRDFIGREALEVQREHGTEKLVGLVMTEKGVLRNELPVRF 300
           DE+++PLAANMGWTIAWEPADRDFIGREALE  +  G++KLVGLVM EKGVLR+++PV F
Sbjct: 241 DESVNPLAANMGWTIAWEPADRDFIGREALEAIKAKGSDKLVGLVMEEKGVLRHDMPVFF 300

Query: 301 TDAQGNQHEGIITSGTFSPTLGYSIALARVPEGIGETAIVQIRNREMPVKVTKPVFVRNG 360
           TDA G +H+G+ITSGTFSPTLGYSIA+ARVP  IGETA V++R + + V+V  P FVRNG
Sbjct: 301 TDANGVEHQGVITSGTFSPTLGYSIAMARVPGAIGETAEVEMRKKRVTVRVIAPSFVRNG 360

Query: 361 K 361
           K
Sbjct: 361 K 361


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: 477
Number of extensions: 12
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 6938618 Sama_2721 (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.20673.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
     1e-144  467.9   0.1   1.1e-144  467.7   0.1    1.0  1  lcl|FitnessBrowser__SB2B:6938618  Sama_2721 glycine cleavage syste


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SB2B:6938618  Sama_2721 glycine cleavage system aminomethyltransferase T (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  467.7   0.1  1.1e-144  1.1e-144       2     362 .]       3     359 ..       2     359 .. 0.98

  Alignments for each domain:
  == domain 1  score: 467.7 bits;  conditional E-value: 1.1e-144
                         TIGR00528   2 krtpLydlhtelggklvdfaGwelPvqykslieeheavrtkaGlfDvshmgkvelsGskslkfLqrllanDvdaLtk 78 
                                       ++t L+  h e  +k+vdf+Gw++P++y+s+ieeh+avr +aG+fDvshm+ v+++G ++++fL++llanD+++Lt+
  lcl|FitnessBrowser__SB2B:6938618   3 NKTVLFSKHLESNAKMVDFHGWNMPLNYGSQIEEHHAVRRDAGMFDVSHMTVVDVEGADARAFLRKLLANDIAKLTV 79 
                                       79**************************************************************************9 PP

                         TIGR00528  79 .GkaqysvllnaqGGvvDDlivykegednrfllvvnaataekDlewlkehleeevtldtlskeisllalqGP....k 150
                                        Gka+y ++ln +GGv+DDli y+ ++  ++++vvn+at+ekDl+w+ e+++++   +t + e++++a+qGP    k
  lcl|FitnessBrowser__SB2B:6938618  80 pGKALYGGMLNHDGGVIDDLITYYLSDT-QYRVVVNSATREKDLAWIGEQAKGFDVTITERPELAMIAVQGPnakaK 155
                                       9************************999.9******************************************99999 PP

                         TIGR00528 151 aktiledlldkaveglkefffvqeaelalkkaliartGytGedGfeiavanekavelwkklveaygvkPiGLgarDt 227
                                       a+t++   +++aveg+k+ff+ q++ l     +ia+tGytGe+G+ei+v++ +a  lw++l++a gv+P+GLgarDt
  lcl|FitnessBrowser__SB2B:6938618 156 AATVFTAEQNAAVEGMKPFFGKQAGSL-----FIATTGYTGEAGYEIIVPEAEAEALWQALLDA-GVQPCGLGARDT 226
                                       99*************************.....********************************.************ PP

                         TIGR00528 228 LrleagmaLyGqeldeeitPleaglgwvvkkerkksdfiGravleeqkengtekklvGlemlekgiarnelkvllt. 303
                                       Lrleagm+LyGq++de++ Pl+a++gw++++e++++dfiGr++le  k++g++k lvGl+m ekg++r++++v++t 
  lcl|FitnessBrowser__SB2B:6938618 227 LRLEAGMNLYGQDMDESVNPLAANMGWTIAWEPADRDFIGREALEAIKAKGSDK-LVGLVMEEKGVLRHDMPVFFTd 302
                                       ***************************************************998.********************96 PP

                         TIGR00528 304 .ngekevGivtsGtlsPtLgknialayvdkelekiGtklevevrnklvkikvvkklfvrs 362
                                        ng ++ G++tsGt+sPtLg++ia+a+v+     iG+++eve+r+k v ++v+ + fvr+
  lcl|FitnessBrowser__SB2B:6938618 303 aNGVEHQGVITSGTFSPTLGYSIAMARVP---GAIGETAEVEMRKKRVTVRVIAPSFVRN 359
                                       66779************************...89***********************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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 8.05
//
[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:

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:

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:

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, or view the source code.

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