Alignments for a candidate for gcvT in Halomonas desiderata SP1

GapMind for catabolism of small carbon sources

Alignments for a candidate for gcvT in Halomonas desiderata SP1

Align Aminomethyltransferase (EC 2.1.2.10) (characterized)
to candidate WP_086511405.1 BZY95_RS18710 glycine cleavage system aminomethyltransferase T

Query= reanno::pseudo13_GW456_L13:PfGW456L13_1866
         (374 letters)



>NCBI__GCF_002151265.1:WP_086511405.1
          Length = 370

 Score =  454 bits (1169), Expect = e-132
 Identities = 238/370 (64%), Positives = 282/370 (76%), Gaps = 4/370 (1%)

Query: 6   LLKTPLHALHIELGARMVPFAGYDMPVQYPLGVMKEHQHTRDQAGLFDVSHMGQIRLTGA 65
           L +TPL+ LH+ELG +MVPFAGY+MPVQ+PLGV KEH+HTR+  GLFDVSHMGQ+ L G 
Sbjct: 4   LKRTPLYDLHLELGGKMVPFAGYEMPVQFPLGVKKEHEHTRNACGLFDVSHMGQLLLHGP 63

Query: 66  NAAKALETLVPVDIIDLPVGMQRYAMFTNATGGILDDLMVANLGNDELFLVVNAACKDQD 125
           N A+ALETLV  DI+ LP GMQRYA+FT   GGILDDLMVAN G D L+LVVNAACKDQD
Sbjct: 64  NPAEALETLVCADIVGLPQGMQRYALFTAQEGGILDDLMVANPG-DHLYLVVNAACKDQD 122

Query: 126 LAHLRKHIGDQCTIEPLFEERALLALQGPAAVTVLARLAPEVAKMTFMQFARVKLLGVDC 185
           +A L   + D+  +E L  +RALLALQGP A  V+ R  P+  ++ FMQ  R +L GV  
Sbjct: 123 IALLDMGLDDEHRVEVL--DRALLALQGPKAADVMRRHCPQACELVFMQHGRFELAGVPV 180

Query: 186 FVSRSGYTGEDGFEISVPATNAEALARALLAEAEVAAIGLGARDSLRLEAGLCLYGHDMN 245
           +VSRSGYTGEDGFEISVPA  AEALAR LLAE EV AIGLGARDSLRLEAGLCLYGHD++
Sbjct: 181 WVSRSGYTGEDGFEISVPAEEAEALARRLLAEEEVEAIGLGARDSLRLEAGLCLYGHDID 240

Query: 246 TDTTPIEASLLWAISKPRRADGARAGGFPGAETVFAQQQA-GVSRKRVGLLPQERTPVRE 304
           T+TTP+EA L+WAI K RR  G R  GFPGA+ +  Q  A    RKRVGLL + R PVRE
Sbjct: 241 TETTPVEAGLVWAIGKARRHGGERPAGFPGADVILHQVDAKDHRRKRVGLLGEGRAPVRE 300

Query: 305 GAEIVNEAGDIIGSVCSGGFGPTLGGPLAMGYVDSAYIALDTPVWAIVRGKKVPLLVSKM 364
           GA++ +E G  IG V SGGFGP++G P+AMGYVD  +  + T V A VRGK++P++VSKM
Sbjct: 301 GADLYDENGHHIGRVTSGGFGPSVGMPVAMGYVDVEHAEIGTTVHAEVRGKRLPMVVSKM 360

Query: 365 PFVPQRYYRG 374
           PFV   YYRG
Sbjct: 361 PFVAPGYYRG 370


Lambda     K      H
   0.321    0.138    0.405 

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: 499
Number of extensions: 20
Number of successful extensions: 4
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: 370
Length adjustment: 30
Effective length of query: 344
Effective length of database: 340
Effective search space:   116960
Effective search space used:   116960
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_086511405.1 BZY95_RS18710 (glycine cleavage system aminomethyltransferase 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.12899.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.2e-105  339.4   0.0   1.3e-105  339.2   0.0    1.0  1  lcl|NCBI__GCF_002151265.1:WP_086511405.1  BZY95_RS18710 glycine cleavage s


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002151265.1:WP_086511405.1  BZY95_RS18710 glycine cleavage system aminomethyltransferase T
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  339.2   0.0  1.3e-105  1.3e-105       1     360 [.       4     363 ..       4     365 .. 0.94

  Alignments for each domain:
  == domain 1  score: 339.2 bits;  conditional E-value: 1.3e-105
                                 TIGR00528   1 lkrtpLydlhtelggklvdfaGwelPvqyk.slieeheavrtkaGlfDvshmgkvelsGskslkfLqrl 68 
                                               lkrtpLydlh elggk+v+faG+e+Pvq+  ++++ehe +r++ GlfDvshmg+  l G++  ++L+ l
  lcl|NCBI__GCF_002151265.1:WP_086511405.1   4 LKRTPLYDLHLELGGKMVPFAGYEMPVQFPlGVKKEHEHTRNACGLFDVSHMGQLLLHGPNPAEALETL 72 
                                               69***************************6488************************************ PP

                                 TIGR00528  69 lanDvdaLtkGkaqysvllnaqGGvvDDlivykegednrfllvvnaataekDlewlkehleeevtldtl 137
                                               + +D+  L++G  +y+ +   +GG++DDl+v + g+   ++lvvnaa++++D + l   l++e  ++ l
  lcl|NCBI__GCF_002151265.1:WP_086511405.1  73 VCADIVGLPQGMQRYALFTAQEGGILDDLMVANPGDH--LYLVVNAACKDQDIALLDMGLDDEHRVEVL 139
                                               **********************************998..9**********************9999877 PP

                                 TIGR00528 138 skeisllalqGPkaktiledlldkaveglkefffvqeaelalkkaliartGytGedGfeiavanekave 206
                                                   +llalqGPka+++++    +a e l  + ++ + ela+    ++r+GytGedGfei+v+ e+a  
  lcl|NCBI__GCF_002151265.1:WP_086511405.1 140 D--RALLALQGPKAADVMRRHCPQACE-LVFMQHG-RFELAGVPVWVSRSGYTGEDGFEISVPAEEAEA 204
                                               5..58************9988877764.3333333.677888888************************ PP

                                 TIGR00528 207 lwkklveaygvkPiGLgarDtLrleagmaLyGqeldeeitPleaglgwvvkker.....kksdfiGrav 270
                                               l+++l+++  v  iGLgarD+Lrleag++LyG+++d e+tP+eagl w++ k r     +   f G +v
  lcl|NCBI__GCF_002151265.1:WP_086511405.1 205 LARRLLAEEEVEAIGLGARDSLRLEAGLCLYGHDIDTETTPVEAGLVWAIGKARrhggeRPAGFPGADV 273
                                               ***************************************************999788777789****** PP

                                 TIGR00528 271 leeqkengtekk.lvGlemlekgiarnelkvlltngekevGivtsGtlsPtLgknialayvdkelekiG 338
                                               + +q + + +++ +vGl    +   r++ +++  ng +++G vtsG + P +g+ +a++yvd e ++iG
  lcl|NCBI__GCF_002151265.1:WP_086511405.1 274 ILHQVDAKDHRRkRVGLLGEGRAPVREGADLYDENG-HHIGRVTSGGFGPSVGMPVAMGYVDVEHAEIG 341
                                               ****998877666****999999**********999.******************************** PP

                                 TIGR00528 339 tklevevrnklvkikvvkklfv 360
                                               t+++ evr+k +++ v k++fv
  lcl|NCBI__GCF_002151265.1:WP_086511405.1 342 TTVHAEVRGKRLPMVVSKMPFV 363
                                               *********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (362 nodes)
Target sequences:                          1  (370 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: 10.34
//
[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