Alignments for a candidate for ilvE in Clostridium kluyveri DSM 555

GapMind for catabolism of small carbon sources

Alignments for a candidate for ilvE in Clostridium kluyveri DSM 555

Align Branched-chain amino acid aminotransferase (EC 2.6.1.42) (characterized)
to candidate WP_012103942.1 CKL_RS17630 branched-chain amino acid aminotransferase

Query= reanno::pseudo5_N2C3_1:AO356_22970
         (339 letters)



>NCBI__GCF_000016505.1:WP_012103942.1
          Length = 344

 Score =  503 bits (1296), Expect = e-147
 Identities = 232/337 (68%), Positives = 280/337 (83%)

Query: 3   NESINWDKLGFDYIKTDKRYLSHWRDGAWDAGTLTDDNVLHISEGSTALHYGQQCFEGLK 62
           N +I+W++LGFDYIKTD RY+S W+DG+WD G L +DN+L ISEGS ALHYGQQCFEGLK
Sbjct: 4   NINIDWNELGFDYIKTDFRYISVWKDGSWDDGKLVEDNMLTISEGSPALHYGQQCFEGLK 63

Query: 63  AYRCKDGSINLFRPDQNAARMQRSCARLLMPQVETEQFVEACKQVVRANERFIPPYGTGG 122
            YR KDG I LFRPDQNA R+  SC RLLMP++  E+F+ AC QV +ANE ++ P+GTG 
Sbjct: 64  CYRRKDGKIQLFRPDQNAKRLNNSCRRLLMPEIPEEKFISACVQVAKANEEYVAPHGTGA 123

Query: 123 ALYLRPFVIGVGDNIGVRTAPEFIFSIFCIPVGAYFKGGLTPHNFLISSFDRAAPQGTGA 182
            LY+RPF+IGVGDNIGV+ A E+IF +FC PVG YFKGG+TP NF+IS +DRAAP GTGA
Sbjct: 124 TLYIRPFIIGVGDNIGVKPAEEYIFCVFCCPVGPYFKGGVTPVNFMISDYDRAAPYGTGA 183

Query: 183 AKVGGNYAASLMPGSQAKKASFADCIYLDPMTHSKIEEVGSANFFGITHDNTFVTPRSPS 242
           AKVGGNYAASL+P   + K  FADCIYLDP TH+KIEEVG+ANFFGIT DN FVTP+SPS
Sbjct: 184 AKVGGNYAASLLPHENSAKRGFADCIYLDPATHTKIEEVGAANFFGITKDNKFVTPKSPS 243

Query: 243 VLPGITRLSLIELAKSRLGLEVIEGDVFIDKLSDFKEAGACGTAAVITPIGGISYKDKLH 302
           +LP IT+ SL+ +AK  LG++V E DV+IDK+ +F EAGACGTAAVITPIGGI YKDKLH
Sbjct: 244 ILPSITKYSLLYIAKEYLGMQVEERDVYIDKIYEFAEAGACGTAAVITPIGGIEYKDKLH 303

Query: 303 VFHSETEVGPITQKLYKELTGVQTGDVEAPAGWIVKV 339
           VF+SETEVGP+T+KLY  L G+Q GDV+AP GWI+++
Sbjct: 304 VFYSETEVGPVTKKLYDTLYGIQFGDVKAPQGWIIEI 340


Lambda     K      H
   0.320    0.138    0.422 

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: 484
Number of extensions: 14
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: 339
Length of database: 344
Length adjustment: 29
Effective length of query: 310
Effective length of database: 315
Effective search space:    97650
Effective search space used:    97650
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_012103942.1 CKL_RS17630 (branched-chain amino acid aminotransferase)
to HMM TIGR01123 (ilvE: branched-chain amino acid aminotransferase (EC 2.6.1.42))

# 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/TIGR01123.hmm
# target sequence database:        /tmp/gapView.453570.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01123  [M=313]
Accession:   TIGR01123
Description: ilvE_II: branched-chain amino acid aminotransferase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.7e-143  461.5   0.0   6.4e-143  461.4   0.0    1.0  1  NCBI__GCF_000016505.1:WP_012103942.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000016505.1:WP_012103942.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  461.4   0.0  6.4e-143  6.4e-143       1     313 []      32     340 ..      32     340 .. 0.99

  Alignments for each domain:
  == domain 1  score: 461.4 bits;  conditional E-value: 6.4e-143
                             TIGR01123   1 WdeaelaseaeleldegsavlhYgqevfeGlkayRtadGkillfRpdanakRlrrsaerlllPeleeelflea 73 
                                           Wd+++l++++ l+++egs +lhYgq++feGlk yR +dGki lfRpd+nakRl++s++rll+Pe++ee f+ a
  NCBI__GCF_000016505.1:WP_012103942.1  32 WDDGKLVEDNMLTISEGSPALHYGQQCFEGLKCYRRKDGKIQLFRPDQNAKRLNNSCRRLLMPEIPEEKFISA 104
                                           ************************************************************************* PP

                             TIGR01123  74 lkqlvkadkdwvpkakseasLYlRPfliatednlGvkaakeylflvlasPvGaYfkgglapvsifveteyvRa 146
                                           + q+ ka++++v++++++a+LY+RPf+i+++dn+Gvk+a+ey+f+v+++PvG+Yfkgg++p  +f+ ++y+Ra
  NCBI__GCF_000016505.1:WP_012103942.1 105 CVQVAKANEEYVAPHGTGATLYIRPFIIGVGDNIGVKPAEEYIFCVFCCPVGPYFKGGVTP-VNFMISDYDRA 176
                                           *************************************************************.788899***** PP

                             TIGR01123 147 apkGtGavkvgGnYaasllaqkkaaeqglddvvyldpvekkkieevGaaniflitkdgelvttplsesiLegv 219
                                           ap GtGa+kvgGnYaasll++++ a++g++d++yldp++++kieevGaan+f+itkd ++++tp+s+siL+++
  NCBI__GCF_000016505.1:WP_012103942.1 177 APYGTGAAKVGGNYAASLLPHENSAKRGFADCIYLDPATHTKIEEVGAANFFGITKD-NKFVTPKSPSILPSI 248
                                           *********************************************************.*************** PP

                             TIGR01123 220 tresllelakd.lgleveereiaidelkaaveaGeivfacGtaavitPvgelkiegkevevkse.evGevtkk 290
                                           t++sll +ak+ lg++veer+++id++++++eaG    acGtaavitP+g+++ ++k ++++se evG+vtkk
  NCBI__GCF_000016505.1:WP_012103942.1 249 TKYSLLYIAKEyLGMQVEERDVYIDKIYEFAEAG----ACGTAAVITPIGGIEYKDKLHVFYSEtEVGPVTKK 317
                                           **********************************....************************999******** PP

                             TIGR01123 291 lrdeltdiqyGkledkegWivev 313
                                           l+d+l +iq+G++++++gWi+e+
  NCBI__GCF_000016505.1:WP_012103942.1 318 LYDTLYGIQFGDVKAPQGWIIEI 340
                                           ********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (313 nodes)
Target sequences:                          1  (344 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: 23.97
//
[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