Alignments for a candidate for gcvT in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Alignments for a candidate for gcvT in Pseudomonas simiae WCS417

Align Aminomethyltransferase (EC 2.1.2.10) (characterized)
to candidate GFF4369 PS417_22370 glycine cleavage system protein T

Query= reanno::WCS417:GFF4369
         (374 letters)



>FitnessBrowser__WCS417:GFF4369
          Length = 374

 Score =  738 bits (1905), Expect = 0.0
 Identities = 374/374 (100%), Positives = 374/374 (100%)

Query: 1   MSTETLLKTPLHALHIELGARMVPFAGYDMPVQYPLGVMKEHLHTRDQAGLFDVSHMGQI 60
           MSTETLLKTPLHALHIELGARMVPFAGYDMPVQYPLGVMKEHLHTRDQAGLFDVSHMGQI
Sbjct: 1   MSTETLLKTPLHALHIELGARMVPFAGYDMPVQYPLGVMKEHLHTRDQAGLFDVSHMGQI 60

Query: 61  RLTGANAAKALETLVPVDILDLPVGMQRYAMFTNDQGGILDDLMVANLGNEELFLVVNAA 120
           RLTGANAAKALETLVPVDILDLPVGMQRYAMFTNDQGGILDDLMVANLGNEELFLVVNAA
Sbjct: 61  RLTGANAAKALETLVPVDILDLPVGMQRYAMFTNDQGGILDDLMVANLGNEELFLVVNAA 120

Query: 121 CKDQDLAHLRQHIGDQCTIEPLFEERALLALQGPAAVKVLARLAPEVTKMTFMQFATLRL 180
           CKDQDLAHLRQHIGDQCTIEPLFEERALLALQGPAAVKVLARLAPEVTKMTFMQFATLRL
Sbjct: 121 CKDQDLAHLRQHIGDQCTIEPLFEERALLALQGPAAVKVLARLAPEVTKMTFMQFATLRL 180

Query: 181 LGVDCYVSRSGYTGEDGFEISVPAANAESLARSLLAETEVQAIGLGARDSLRLEAGLCLY 240
           LGVDCYVSRSGYTGEDGFEISVPAANAESLARSLLAETEVQAIGLGARDSLRLEAGLCLY
Sbjct: 181 LGVDCYVSRSGYTGEDGFEISVPAANAESLARSLLAETEVQAIGLGARDSLRLEAGLCLY 240

Query: 241 GHDMNTDTTPIEASLLWAISKARRADGARAGGFPGADTIFTQQQAGVSRKRVGLLPQERT 300
           GHDMNTDTTPIEASLLWAISKARRADGARAGGFPGADTIFTQQQAGVSRKRVGLLPQERT
Sbjct: 241 GHDMNTDTTPIEASLLWAISKARRADGARAGGFPGADTIFTQQQAGVSRKRVGLLPQERT 300

Query: 301 PVREGAQIVDADGTVIGSVCSGGFGSTLGGPLAMGYLDSAFIALDTEVSALVRGKKVPLR 360
           PVREGAQIVDADGTVIGSVCSGGFGSTLGGPLAMGYLDSAFIALDTEVSALVRGKKVPLR
Sbjct: 301 PVREGAQIVDADGTVIGSVCSGGFGSTLGGPLAMGYLDSAFIALDTEVSALVRGKKVPLR 360

Query: 361 VSKMPFVPQRYYRG 374
           VSKMPFVPQRYYRG
Sbjct: 361 VSKMPFVPQRYYRG 374


Lambda     K      H
   0.321    0.137    0.398 

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: 643
Number of extensions: 21
Number of successful extensions: 3
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: 374
Length of database: 374
Length adjustment: 30
Effective length of query: 344
Effective length of database: 344
Effective search space:   118336
Effective search space used:   118336
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: 50 (23.9 bits)

Align candidate GFF4369 PS417_22370 (glycine cleavage system protein T)
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.18283.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
     2e-107  345.2   0.0   2.3e-107  345.0   0.0    1.0  1  lcl|FitnessBrowser__WCS417:GFF4369  PS417_22370 glycine cleavage sys


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF4369  PS417_22370 glycine cleavage system protein T
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  345.0   0.0  2.3e-107  2.3e-107       2     361 ..       7     368 ..       6     369 .. 0.96

  Alignments for each domain:
  == domain 1  score: 345.0 bits;  conditional E-value: 2.3e-107
                           TIGR00528   2 krtpLydlhtelggklvdfaGwelPvqyk.slieeheavrtkaGlfDvshmgkvelsGskslkfLqrllanDvda 75 
                                          +tpL+ lh elg+++v+faG+ +Pvqy  ++++eh  +r++aGlfDvshmg+++l+G ++ k+L+ l++ D+  
  lcl|FitnessBrowser__WCS417:GFF4369   7 LKTPLHALHIELGARMVPFAGYDMPVQYPlGVMKEHLHTRDQAGLFDVSHMGQIRLTGANAAKALETLVPVDILD 81 
                                         79**************************6488******************************************* PP

                           TIGR00528  76 LtkGkaqysvllnaqGGvvDDlivykegednrfllvvnaataekDlewlkehleeevtldtlskeisllalqGPk 150
                                         L++G  +y+ + n qGG++DDl+v + g++ ++ lvvnaa++++Dl++l++h+ ++ t++ l +e +llalqGP 
  lcl|FitnessBrowser__WCS417:GFF4369  82 LPVGMQRYAMFTNDQGGILDDLMVANLGNE-ELFLVVNAACKDQDLAHLRQHIGDQCTIEPLFEERALLALQGPA 155
                                         ****************************99.999***************************************** PP

                           TIGR00528 151 aktiledlldkaveglkefffvqeaelalkkaliartGytGedGfeiavanekavelwkklveaygvkPiGLgar 225
                                         a ++l  l   +v+++  + f     l++ +++++r+GytGedGfei+v+  +a  l+++l+++  v+ iGLgar
  lcl|FitnessBrowser__WCS417:GFF4369 156 AVKVLARLAP-EVTKMTFMQFA-TLRLLGVDCYVSRSGYTGEDGFEISVPAANAESLARSLLAETEVQAIGLGAR 228
                                         *****99875.45566544444.5578899********************************************* PP

                           TIGR00528 226 DtLrleagmaLyGqeldeeitPleaglgwvvkker.....kksdfiGravleeqkengtekklvGlemlekgiar 295
                                         D+Lrleag++LyG++++ ++tP+ea+l w+++k r     +   f G +++  q++ g+ +k+vGl   e+   r
  lcl|FitnessBrowser__WCS417:GFF4369 229 DSLRLEAGLCLYGHDMNTDTTPIEASLLWAISKARradgaRAGGFPGADTIFTQQQAGVSRKRVGLLPQERTPVR 303
                                         *********************************99888877889******************************* PP

                           TIGR00528 296 nelkvlltngekevGivtsGtlsPtLgknialayvdkelekiGtklevevrnklvkikvvkklfvr 361
                                         ++ +++ ++g + +G v sG +  tLg  +a++y+d+ +    t++   vr+k+v+++v k++fv+
  lcl|FitnessBrowser__WCS417:GFF4369 304 EGAQIVDADG-TVIGSVCSGGFGSTLGGPLAMGYLDSAFIALDTEVSALVRGKKVPLRVSKMPFVP 368
                                         **********.*****************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (362 nodes)
Target sequences:                          1  (374 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 12.07
//
[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