Alignments for a candidate for gcvT in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for gcvT in Klebsiella michiganensis M5al

Align Aminomethyltransferase (EC 2.1.2.10) (characterized)
to candidate BWI76_RS23880 BWI76_RS23880 glycine cleavage system protein T

Query= reanno::Koxy:BWI76_RS23880
         (364 letters)



>FitnessBrowser__Koxy:BWI76_RS23880
          Length = 364

 Score =  729 bits (1883), Expect = 0.0
 Identities = 364/364 (100%), Positives = 364/364 (100%)

Query: 1   MAQQTPLFEQHTLCGARMVDFHGWMMPLHYGSQIDEHHAVRGDAGMFDVSHMTIVDFHGS 60
           MAQQTPLFEQHTLCGARMVDFHGWMMPLHYGSQIDEHHAVRGDAGMFDVSHMTIVDFHGS
Sbjct: 1   MAQQTPLFEQHTLCGARMVDFHGWMMPLHYGSQIDEHHAVRGDAGMFDVSHMTIVDFHGS 60

Query: 61  RIREFLRYLLANDVAKLTVPGKALYSGMLTASGGVIDDLIVYFLSEDYFRLVVNSATREK 120
           RIREFLRYLLANDVAKLTVPGKALYSGMLTASGGVIDDLIVYFLSEDYFRLVVNSATREK
Sbjct: 61  RIREFLRYLLANDVAKLTVPGKALYSGMLTASGGVIDDLIVYFLSEDYFRLVVNSATREK 120

Query: 121 DLAWIAQQSESYGLEITVRDDLSLIAVQGPRAKEKAATLFTDAQRQAVEGMKPFFGVQAG 180
           DLAWIAQQSESYGLEITVRDDLSLIAVQGPRAKEKAATLFTDAQRQAVEGMKPFFGVQAG
Sbjct: 121 DLAWIAQQSESYGLEITVRDDLSLIAVQGPRAKEKAATLFTDAQRQAVEGMKPFFGVQAG 180

Query: 181 DLFIATTGYTGEAGYEIALPNEQAVDFWRGLLDAGVKPCGLGARDTLRLEAGMNLYGQEM 240
           DLFIATTGYTGEAGYEIALPNEQAVDFWRGLLDAGVKPCGLGARDTLRLEAGMNLYGQEM
Sbjct: 181 DLFIATTGYTGEAGYEIALPNEQAVDFWRGLLDAGVKPCGLGARDTLRLEAGMNLYGQEM 240

Query: 241 DEGVSPLAANMGWTIAWEPTDRDFIGREALEMQREKGTEQLVGLVMTEKGVLRGGLPVRF 300
           DEGVSPLAANMGWTIAWEPTDRDFIGREALEMQREKGTEQLVGLVMTEKGVLRGGLPVRF
Sbjct: 241 DEGVSPLAANMGWTIAWEPTDRDFIGREALEMQREKGTEQLVGLVMTEKGVLRGGLPVRF 300

Query: 301 SDADGNQKEGIITSGTFSPTLGYSIALARVPEGIGETAVVQIRNREMPVKVTKPVFVRNG 360
           SDADGNQKEGIITSGTFSPTLGYSIALARVPEGIGETAVVQIRNREMPVKVTKPVFVRNG
Sbjct: 301 SDADGNQKEGIITSGTFSPTLGYSIALARVPEGIGETAVVQIRNREMPVKVTKPVFVRNG 360

Query: 361 KAVV 364
           KAVV
Sbjct: 361 KAVV 364


Lambda     K      H
   0.320    0.137    0.407 

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: 672
Number of extensions: 13
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 BWI76_RS23880 BWI76_RS23880 (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.25440.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   2.3e-162  525.9   0.0   2.6e-162  525.8   0.0    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS23880  BWI76_RS23880 glycine cleavage s


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS23880  BWI76_RS23880 glycine cleavage system protein T
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  525.8   0.0  2.6e-162  2.6e-162       1     362 []       2     359 ..       2     359 .. 0.99

  Alignments for each domain:
  == domain 1  score: 525.8 bits;  conditional E-value: 2.6e-162
                               TIGR00528   1 lkrtpLydlhtelggklvdfaGwelPvqykslieeheavrtkaGlfDvshmgkvelsGskslkfLqrllan 71 
                                             +++tpL+++ht +g+++vdf+Gw++P++y+s+i+eh+avr +aG+fDvshm++v+  Gs+ ++fL++llan
  lcl|FitnessBrowser__Koxy:BWI76_RS23880   2 AQQTPLFEQHTLCGARMVDFHGWMMPLHYGSQIDEHHAVRGDAGMFDVSHMTIVDFHGSRIREFLRYLLAN 72 
                                             68********************************************************************* PP

                               TIGR00528  72 DvdaLtk.GkaqysvllnaqGGvvDDlivykegednrfllvvnaataekDlewlkehleeevtldtlskei 141
                                             Dv++Lt+ Gka+ys++l a+GGv+DDlivy  +ed  f+lvvn+at+ekDl+w+ ++ e  + ++t+++++
  lcl|FitnessBrowser__Koxy:BWI76_RS23880  73 DVAKLTVpGKALYSGMLTASGGVIDDLIVYFLSED-YFRLVVNSATREKDLAWIAQQSESYGLEITVRDDL 142
                                             ******99***************************.*********************************** PP

                               TIGR00528 142 sllalqGP....kaktiledlldkaveglkefffvqeaelalkkaliartGytGedGfeiavanekavelw 208
                                             sl+a+qGP    ka+t++ d++++aveg+k+ff+vq+++l     +ia+tGytGe+G+eia++ne+av++w
  lcl|FitnessBrowser__Koxy:BWI76_RS23880 143 SLIAVQGPrakeKAATLFTDAQRQAVEGMKPFFGVQAGDL-----FIATTGYTGEAGYEIALPNEQAVDFW 208
                                             ********9999999*************************.....************************** PP

                               TIGR00528 209 kklveaygvkPiGLgarDtLrleagmaLyGqeldeeitPleaglgwvvkkerkksdfiGravleeqkengt 279
                                             + l++a gvkP+GLgarDtLrleagm+LyGqe+de ++Pl+a++gw++++e++++dfiGr++le q+e+gt
  lcl|FitnessBrowser__Koxy:BWI76_RS23880 209 RGLLDA-GVKPCGLGARDTLRLEAGMNLYGQEMDEGVSPLAANMGWTIAWEPTDRDFIGREALEMQREKGT 278
                                             ******.**************************************************************** PP

                               TIGR00528 280 ekklvGlemlekgiarnelkvllt..ngekevGivtsGtlsPtLgknialayvdkelekiGtklevevrnk 348
                                             e+ lvGl+m+ekg++r +l+v+++  +g++++Gi+tsGt+sPtLg++iala+v+   e+iG+++ v++rn+
  lcl|FitnessBrowser__Koxy:BWI76_RS23880 279 EQ-LVGLVMTEKGVLRGGLPVRFSdaDGNQKEGIITSGTFSPTLGYSIALARVP---EGIGETAVVQIRNR 345
                                             *9.*******************997789**************************...99************ PP

                               TIGR00528 349 lvkikvvkklfvrs 362
                                             ++++kv+k++fvr+
  lcl|FitnessBrowser__Koxy:BWI76_RS23880 346 EMPVKVTKPVFVRN 359
                                             ************96 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 10.80
//
[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