Alignments for a candidate for gcvT in Thiomicrorhabdus arctica DSM 13458

GapMind for catabolism of small carbon sources

Alignments for a candidate for gcvT in Thiomicrorhabdus arctica DSM 13458

Align Aminomethyltransferase (EC 2.1.2.10) (characterized)
to candidate WP_019556678.1 F612_RS0105115 glycine cleavage system aminomethyltransferase GcvT

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



>NCBI__GCF_000381085.1:WP_019556678.1
          Length = 375

 Score =  486 bits (1250), Expect = e-142
 Identities = 242/370 (65%), Positives = 294/370 (79%), Gaps = 2/370 (0%)

Query: 5   TLLKTPLHALHIELGARMVPFAGYDMPVQYPLGVMKEHLHTRDQAGLFDVSHMGQIRLTG 64
           TL +TPL++LH ELGA++VPFAGY MPVQYPLG+ KEHLHTR +AGLFDVSHMGQ+RLTG
Sbjct: 8   TLKQTPLYSLHQELGAKLVPFAGYLMPVQYPLGIKKEHLHTRQKAGLFDVSHMGQVRLTG 67

Query: 65  ANAAKALETLVPVDILDLPVGMQRYAMFTNDQGGILDDLMVANLGNEELFLVVNAACKDQ 124
            N A ALE LVPVDI+DLP   QRYA+FTN+QGG++DDLMV N G + LFLVVNAACK Q
Sbjct: 68  KNVATALEALVPVDIVDLPKMQQRYALFTNEQGGVMDDLMVTNAG-DYLFLVVNAACKAQ 126

Query: 125 DLAHLRQHIGDQCTIEPLFEERALLALQGPAAVKVLARLAPEVTKMTFMQFATLRLLGVD 184
           D+AHL++H+ DQC I+ L ++RALLALQGP A +VLA+ APE  +M FM   TL + G++
Sbjct: 127 DIAHLQKHLADQCEIDVL-DDRALLALQGPLAGEVLAKFAPESAEMIFMSAKTLLVNGIE 185

Query: 185 CYVSRSGYTGEDGFEISVPAANAESLARSLLAETEVQAIGLGARDSLRLEAGLCLYGHDM 244
           C+V+RSGYTGEDGFEISV    AE LAR+LLA+  V+ IGLGARDSLRLEAGLCLYGHD+
Sbjct: 186 CFVTRSGYTGEDGFEISVANREAEGLARALLADDAVEMIGLGARDSLRLEAGLCLYGHDL 245

Query: 245 NTDTTPIEASLLWAISKARRADGARAGGFPGADTIFTQQQAGVSRKRVGLLPQERTPVRE 304
             DT+P+EASLLWA+SK+RRADG R GG+ GA+ I  Q   GVSRKR+GL P  + PVR+
Sbjct: 246 ENDTSPVEASLLWALSKSRRADGVRPGGYIGAEVIMAQMANGVSRKRIGLKPLGKMPVRD 305

Query: 305 GAQIVDADGTVIGSVCSGGFGSTLGGPLAMGYLDSAFIALDTEVSALVRGKKVPLRVSKM 364
           GA++VD    +IG V SGGF  TL  P+AMGY+ + F  + T++ ALVR KKVPL V K+
Sbjct: 306 GAEVVDDQDNIIGFVTSGGFSVTLNCPVAMGYVQTEFAQVGTKLQALVRNKKVPLEVVKL 365

Query: 365 PFVPQRYYRG 374
           PFV Q YYRG
Sbjct: 366 PFVKQNYYRG 375


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: 448
Number of extensions: 17
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: 375
Length adjustment: 30
Effective length of query: 344
Effective length of database: 345
Effective search space:   118680
Effective search space used:   118680
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 WP_019556678.1 F612_RS0105115 (glycine cleavage system aminomethyltransferase GcvT)
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.1131064.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   7.2e-114  366.4   0.0   8.2e-114  366.2   0.0    1.0  1  NCBI__GCF_000381085.1:WP_019556678.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000381085.1:WP_019556678.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  366.2   0.0  8.2e-114  8.2e-114       1     361 [.       9     369 ..       9     370 .. 0.94

  Alignments for each domain:
  == domain 1  score: 366.2 bits;  conditional E-value: 8.2e-114
                             TIGR00528   1 lkrtpLydlhtelggklvdfaGwelPvqyk.slieeheavrtkaGlfDvshmgkvelsGskslkfLqrllanD 72 
                                           lk+tpLy lh+elg+klv+faG+ +Pvqy  ++++eh  +r+kaGlfDvshmg+v+l+G+++ ++L+ l++ D
  NCBI__GCF_000381085.1:WP_019556678.1   9 LKQTPLYSLHQELGAKLVPFAGYLMPVQYPlGIKKEHLHTRQKAGLFDVSHMGQVRLTGKNVATALEALVPVD 81 
                                           69***************************6489**************************************** PP

                             TIGR00528  73 vdaLtkGkaqysvllnaqGGvvDDlivykegednrfllvvnaataekDlewlkehleeevtldtlskeislla 145
                                           +  L+k + +y+ + n qGGv+DDl+v++ g+   + lvvnaa++ +D ++l++hl+++ ++d + ++ +lla
  NCBI__GCF_000381085.1:WP_019556678.1  82 IVDLPKMQQRYALFTNEQGGVMDDLMVTNAGDY--LFLVVNAACKAQDIAHLQKHLADQCEID-VLDDRALLA 151
                                           *****************************9998..99*********************99887.567889*** PP

                             TIGR00528 146 lqGPkaktiledlldkaveglkefffvqeael..alkkaliartGytGedGfeiavanekavelwkklveayg 216
                                           lqGP a ++l +   +++e    + f+ ++ l   + +++++r+GytGedGfei+van +a  l+++l+++ +
  NCBI__GCF_000381085.1:WP_019556678.1 152 LQGPLAGEVLAKFAPESAE----MIFMSAKTLlvNGIECFVTRSGYTGEDGFEISVANREAEGLARALLADDA 220
                                           *********9988776665....4455444440044577********************************** PP

                             TIGR00528 217 vkPiGLgarDtLrleagmaLyGqeldeeitPleaglgwvvkker.....kksdfiGravleeqkengtekklv 284
                                           v  iGLgarD+Lrleag++LyG++l+++++P+ea+l w+++k+r     +   +iG +v++ q +ng+ +k++
  NCBI__GCF_000381085.1:WP_019556678.1 221 VEMIGLGARDSLRLEAGLCLYGHDLENDTSPVEASLLWALSKSRradgvRPGGYIGAEVIMAQMANGVSRKRI 293
                                           *******************************************9888777789******************** PP

                             TIGR00528 285 GlemlekgiarnelkvlltngekevGivtsGtlsPtLgknialayvdkelekiGtklevevrnklvkikvvkk 357
                                           Gl+ l k   r++ +v+  + ++++G vtsG +s tL+  +a++yv++e++++Gtkl+  vrnk+v+++vvk 
  NCBI__GCF_000381085.1:WP_019556678.1 294 GLKPLGKMPVRDGAEVVD-DQDNIIGFVTSGGFSVTLNCPVAMGYVQTEFAQVGTKLQALVRNKKVPLEVVKL 365
                                           *****************9.778*************************************************** PP

                             TIGR00528 358 lfvr 361
                                           +fv+
  NCBI__GCF_000381085.1:WP_019556678.1 366 PFVK 369
                                           **98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (362 nodes)
Target sequences:                          1  (375 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 24.37
//
[ok]

This GapMind analysis is from Apr 09 2024. 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 2024 update 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