Alignments for a candidate for gcvT in Clostridium kluyveri DSM 555

GapMind for catabolism of small carbon sources

Alignments for a candidate for gcvT in Clostridium kluyveri DSM 555

Align Aminomethyltransferase (EC 2.1.2.10) (characterized)
to candidate WP_012102169.1 CKL_RS08715 glycine cleavage system protein T

Query= reanno::pseudo6_N2E2:Pf6N2E2_5556
         (374 letters)



>NCBI__GCF_000016505.1:WP_012102169.1
          Length = 362

 Score =  234 bits (598), Expect = 2e-66
 Identities = 146/364 (40%), Positives = 210/364 (57%), Gaps = 15/364 (4%)

Query: 8   KTPLHALHLELGARMVPFAGYDMPVQYPLGVMKEHQHTRDQAGLFDVSHMGQIRLTGAGA 67
           KTPL+  HL+   +MVPFAGY +PVQY  GV+ EH   R   GLFDVSHMG+I   G  A
Sbjct: 4   KTPLYEKHLKYKGKMVPFAGYLLPVQYEGGVIAEHMAVRKVCGLFDVSHMGEITCRGEDA 63

Query: 68  AKALETLVPVDIIDLPVGMQRYAMFTNENGGILDDLMVANLGNDELFLVVNAACKDQDLA 127
            K L  L+  +   +  G  RY+   NE GG++DD++V  + +++  +VVNAA KD+D +
Sbjct: 64  LKNLNHLLTNNFEGMYDGQARYSPMCNEKGGVVDDMIVYKVKDNDYLIVVNAANKDKDYS 123

Query: 128 HLRAHIGAQCSIEPLFEARALLALQGPAAVTVLARL--APDVAKMTFMQFQRVTLLGMDC 185
            +++H       E + E  A +ALQGP++ +V++ +  + ++ K  +      TL G  C
Sbjct: 124 WMKSHGEGNVVFEDISEDVAQIALQGPSSFSVISNVVKSDEIPKKYYSGIFNCTLEGAKC 183

Query: 186 YVSRSGYTGEDGFEISVPAAEAEKLARALL---AEPEVAAIGLGARDSLRLEAGLCLYGH 242
            +S++GYTGEDG+EI + + +A ++  ALL    E  +   GLGARD+LRLEA + LYGH
Sbjct: 184 MISKTGYTGEDGYEIYMESDKAPRIWEALLEAGKEEGLIPCGLGARDTLRLEASMPLYGH 243

Query: 243 DMNTETTPIEASLLWAISKVRRADGARAGGFPGAETVFAQQQGGVKRKRVGLLPQERTPV 302
           +MN E TPIEA L   I K+ + D      F G + +  +Q   +++KRVGL    R  +
Sbjct: 244 EMNDEITPIEAGLGMFI-KMDKKD------FIGKKAL--EQNQPIQKKRVGLKVTGRGII 294

Query: 303 REGAEIVNEAGEIIGTVCSGGFGPTLGGPLAMGYLDSAYVALDTPVWAIVRGKKVPLLVS 362
           RE  E+ +     IG   SG   P +G P AM  L S Y  L T V  I R KK+   V 
Sbjct: 295 RENMEVYS-GDYNIGITTSGTHCPYIGYPAAMALLSSDYSKLGTKVTVIARRKKIEAEVV 353

Query: 363 KMPF 366
           ++PF
Sbjct: 354 ELPF 357


Lambda     K      H
   0.321    0.138    0.406 

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: 368
Number of extensions: 19
Number of successful extensions: 5
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: 362
Length adjustment: 30
Effective length of query: 344
Effective length of database: 332
Effective search space:   114208
Effective search space used:   114208
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_012102169.1 CKL_RS08715 (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.22034.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   6.3e-123  396.2   0.0   7.3e-123  396.0   0.0    1.0  1  lcl|NCBI__GCF_000016505.1:WP_012102169.1  CKL_RS08715 glycine cleavage sys


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000016505.1:WP_012102169.1  CKL_RS08715 glycine cleavage system protein T
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  396.0   0.0  7.3e-123  7.3e-123       2     361 ..       3     359 ..       2     360 .. 0.97

  Alignments for each domain:
  == domain 1  score: 396.0 bits;  conditional E-value: 7.3e-123
                                 TIGR00528   2 krtpLydlhtelggklvdfaGwelPvqyksl.ieeheavrtkaGlfDvshmgkvelsGskslkfLqrll 69 
                                               k+tpLy+ h ++ gk+v+faG+ lPvqy++  i eh avr+  GlfDvshmg+++ +G+++lk L++ll
  lcl|NCBI__GCF_000016505.1:WP_012102169.1   3 KKTPLYEKHLKYKGKMVPFAGYLLPVQYEGGvIAEHMAVRKVCGLFDVSHMGEITCRGEDALKNLNHLL 71 
                                               89**************************8755************************************* PP

                                 TIGR00528  70 anDvdaLtkGkaqysvllnaqGGvvDDlivykegednrfllvvnaataekDlewlkehleeevtldtls 138
                                               +n+++ +  G+a+ys ++n +GGvvDD+ivyk +++  +l+vvnaa+++kD +w+k h e++v ++++s
  lcl|NCBI__GCF_000016505.1:WP_012102169.1  72 TNNFEGMYDGQARYSPMCNEKGGVVDDMIVYKVKDN-DYLIVVNAANKDKDYSWMKSHGEGNVVFEDIS 139
                                               ********************************9999.9******************************* PP

                                 TIGR00528 139 keisllalqGPkaktiledlldkaveglkefffvqeaelalkkaliartGytGedGfeiavanekavel 207
                                               ++++ +alqGP + +++ ++++ +    k + ++ +  l + k++i++tGytGedG+ei+++++ka  +
  lcl|NCBI__GCF_000016505.1:WP_012102169.1 140 EDVAQIALQGPSSFSVISNVVKSDEIPKKYYSGIFNCTLEGAKCMISKTGYTGEDGYEIYMESDKAPRI 208
                                               *********************99999999**************************************** PP

                                 TIGR00528 208 wkklvea...ygvkPiGLgarDtLrleagmaLyGqeldeeitPleaglgwvvkkerkksdfiGravlee 273
                                               w++l+ea    g++P+GLgarDtLrlea+m+LyG+e+++eitP+eaglg  +k++  k+dfiG+++le+
  lcl|NCBI__GCF_000016505.1:WP_012102169.1 209 WEALLEAgkeEGLIPCGLGARDTLRLEASMPLYGHEMNDEITPIEAGLGMFIKMD--KKDFIGKKALEQ 275
                                               *****998889*******************************************9..99*******975 PP

                                 TIGR00528 274 qkengtekklvGlemlekgiarnelkvlltngekevGivtsGtlsPtLgknialayvdkelekiGtkle 342
                                                 ++ ++kk+vGl+++ +gi r++++v+   g+ ++Gi tsGt  P +g+  a+a++ ++++k Gtk++
  lcl|NCBI__GCF_000016505.1:WP_012102169.1 276 --NQPIQKKRVGLKVTGRGIIRENMEVYS--GDYNIGITTSGTHCPYIGYPAAMALLSSDYSKLGTKVT 340
                                               ..5678999*******************9..889*********************************** PP

                                 TIGR00528 343 vevrnklvkikvvkklfvr 361
                                               v  r+k+++++vv  +f++
  lcl|NCBI__GCF_000016505.1:WP_012102169.1 341 VIARRKKIEAEVVELPFYK 359
                                               ******************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (362 nodes)
Target sequences:                          1  (362 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: 10.04
//
[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