Alignments for a candidate for hutH in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutH in Sinorhizobium meliloti 1021

Align Histidine ammonia-lyase (EC 4.3.1.3) (characterized)
to candidate SM_b21165 SM_b21165 histidine ammonia-lyase

Query= reanno::Smeli:SM_b21165
         (511 letters)



>FitnessBrowser__Smeli:SM_b21165
          Length = 511

 Score =  978 bits (2529), Expect = 0.0
 Identities = 511/511 (100%), Positives = 511/511 (100%)

Query: 1   MTVILRPGSVPLSDLETIYWTGAPARLDAAFDAGIAKAAARIAEIVAGNAPVYGINTGFG 60
           MTVILRPGSVPLSDLETIYWTGAPARLDAAFDAGIAKAAARIAEIVAGNAPVYGINTGFG
Sbjct: 1   MTVILRPGSVPLSDLETIYWTGAPARLDAAFDAGIAKAAARIAEIVAGNAPVYGINTGFG 60

Query: 61  KLASIKIDSSDVATLQRNLILSHCCGVGQPLTEDIVRLIMALKLISLGRGASGVRLELVR 120
           KLASIKIDSSDVATLQRNLILSHCCGVGQPLTEDIVRLIMALKLISLGRGASGVRLELVR
Sbjct: 61  KLASIKIDSSDVATLQRNLILSHCCGVGQPLTEDIVRLIMALKLISLGRGASGVRLELVR 120

Query: 121 LIEAMLDKGVIPLIPEKGSVGASGDLAPLAHMAAVMMGHGEAFFAGERMKGDAALKAAGL 180
           LIEAMLDKGVIPLIPEKGSVGASGDLAPLAHMAAVMMGHGEAFFAGERMKGDAALKAAGL
Sbjct: 121 LIEAMLDKGVIPLIPEKGSVGASGDLAPLAHMAAVMMGHGEAFFAGERMKGDAALKAAGL 180

Query: 181 SPVTLAAKEGLALINGTQVSTALALAGLFRAHRAGQAALITGALSTDAAMGSSAPFHPDI 240
           SPVTLAAKEGLALINGTQVSTALALAGLFRAHRAGQAALITGALSTDAAMGSSAPFHPDI
Sbjct: 181 SPVTLAAKEGLALINGTQVSTALALAGLFRAHRAGQAALITGALSTDAAMGSSAPFHPDI 240

Query: 241 HTLRGHKGQIDTAAALRQLLTGSPIRQSHIEGDERVQDPYCIRCQPQVDGACLDLLRSVA 300
           HTLRGHKGQIDTAAALRQLLTGSPIRQSHIEGDERVQDPYCIRCQPQVDGACLDLLRSVA
Sbjct: 241 HTLRGHKGQIDTAAALRQLLTGSPIRQSHIEGDERVQDPYCIRCQPQVDGACLDLLRSVA 300

Query: 301 ATLTIEANAVTDNPLVLSDNSVVSGGNFHAEPVAFAADQIALAVCEIGAISQRRIALLVD 360
           ATLTIEANAVTDNPLVLSDNSVVSGGNFHAEPVAFAADQIALAVCEIGAISQRRIALLVD
Sbjct: 301 ATLTIEANAVTDNPLVLSDNSVVSGGNFHAEPVAFAADQIALAVCEIGAISQRRIALLVD 360

Query: 361 PALSYGLPAFLAKKPGLNSGLMIAEVTSAALMSENKQLSHPASVDSTPTSANQEDHVSMA 420
           PALSYGLPAFLAKKPGLNSGLMIAEVTSAALMSENKQLSHPASVDSTPTSANQEDHVSMA
Sbjct: 361 PALSYGLPAFLAKKPGLNSGLMIAEVTSAALMSENKQLSHPASVDSTPTSANQEDHVSMA 420

Query: 421 CHGARRLLQMTENLFSIIGIEALAAVQGIEFRAPLTTSPELQKAAAAVRGVSSSIEEDRY 480
           CHGARRLLQMTENLFSIIGIEALAAVQGIEFRAPLTTSPELQKAAAAVRGVSSSIEEDRY
Sbjct: 421 CHGARRLLQMTENLFSIIGIEALAAVQGIEFRAPLTTSPELQKAAAAVRGVSSSIEEDRY 480

Query: 481 MADDLKAAGDLVASGRLAAAVSAGILPKLEN 511
           MADDLKAAGDLVASGRLAAAVSAGILPKLEN
Sbjct: 481 MADDLKAAGDLVASGRLAAAVSAGILPKLEN 511


Lambda     K      H
   0.318    0.133    0.372 

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: 975
Number of extensions: 25
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: 511
Length of database: 511
Length adjustment: 35
Effective length of query: 476
Effective length of database: 476
Effective search space:   226576
Effective search space used:   226576
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)

Align candidate SM_b21165 SM_b21165 (histidine ammonia-lyase)
to HMM TIGR01225 (hutH: histidine ammonia-lyase (EC 4.3.1.3))

# 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/TIGR01225.hmm
# target sequence database:        /tmp/gapView.6919.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01225  [M=506]
Accession:   TIGR01225
Description: hutH: histidine ammonia-lyase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
   9.6e-235  765.7   8.3   1.1e-234  765.5   8.3    1.0  1  lcl|FitnessBrowser__Smeli:SM_b21165  SM_b21165 histidine ammonia-lyas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SM_b21165  SM_b21165 histidine ammonia-lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  765.5   8.3  1.1e-234  1.1e-234       1     505 [.       3     508 ..       3     509 .. 0.99

  Alignments for each domain:
  == domain 1  score: 765.5 bits;  conditional E-value: 1.1e-234
                            TIGR01225   1 vvldgesltledleavarekarvelsaaaeeavaksravieeivaedktvYGvntGFGklasvkidkedlaeLq 74 
                                          v+l+++s+ l+dle++++++a+++l+aa+++ +ak++a+i+eiva++++vYG+ntGFGklas+kid++d+a+Lq
  lcl|FitnessBrowser__Smeli:SM_b21165   3 VILRPGSVPLSDLETIYWTGAPARLDAAFDAGIAKAAARIAEIVAGNAPVYGINTGFGKLASIKIDSSDVATLQ 76 
                                          7899********************************************************************** PP

                            TIGR01225  75 rnlvrsHaaGvGepleeevvRallvlrlnslakGysgvraevlellvallnaevlPvvpekGsvGasGDLAPLa 148
                                          rnl++sH++GvG+pl+e++vR++++l+l sl +G+sgvr e+++l+ a+l+++v+P++pekGsvGasGDLAPLa
  lcl|FitnessBrowser__Smeli:SM_b21165  77 RNLILSHCCGVGQPLTEDIVRLIMALKLISLGRGASGVRLELVRLIEAMLDKGVIPLIPEKGSVGASGDLAPLA 150
                                          ************************************************************************** PP

                            TIGR01225 149 hlalvliGeGeaefegevmdaaeaLaaaglePvtlkakEGlALinGtqlmtalavlalvdaekllesadiaaal 222
                                          h+a+v++G+Gea+f+ge+m++++aL+aagl+Pvtl+akEGlALinGtq++tala+++l++a++  ++a i++al
  lcl|FitnessBrowser__Smeli:SM_b21165 151 HMAAVMMGHGEAFFAGERMKGDAALKAAGLSPVTLAAKEGLALINGTQVSTALALAGLFRAHRAGQAALITGAL 224
                                          ************************************************************************** PP

                            TIGR01225 223 sleallgtskafdpdihevrphrgqiavaarlrellagseiaeshk.dedrvqDaYslRciPqvhGavldtldq 295
                                          s++a++g+s++f+pdih++r+h+gqi++aa+lr+ll+gs i++sh  +++rvqD+Y++Rc+Pqv+Ga+ld l++
  lcl|FitnessBrowser__Smeli:SM_b21165 225 STDAAMGSSAPFHPDIHTLRGHKGQIDTAAALRQLLTGSPIRQSHIeGDERVQDPYCIRCQPQVDGACLDLLRS 298
                                          *********************************************999************************** PP

                            TIGR01225 296 vkevlaiElnsatDnPlvfadegevvsgGnFHgepvAlaldflaiaiaelgaiseRRierlldpals.eLppFL 368
                                          v+++l+iE+n++tDnPlv++d+ +vvsgGnFH+epvA+a+d++a+a++e+gais+RRi++l+dpals +Lp+FL
  lcl|FitnessBrowser__Smeli:SM_b21165 299 VAATLTIEANAVTDNPLVLSDN-SVVSGGNFHAEPVAFAADQIALAVCEIGAISQRRIALLVDPALSyGLPAFL 371
                                          *********************8.*************************************************** PP

                            TIGR01225 369 aedsGlnsGlmiaqytaAaLvsenkaLahPasvDsiptsanqEDHvsmgaaaarkllevvenvrrviaiEllaa 442
                                          a+++GlnsGlmia++t+AaL+senk+L+hPasvDs+ptsanqEDHvsm++++ar+ll+++en+ ++i+iE+laa
  lcl|FitnessBrowser__Smeli:SM_b21165 372 AKKPGLNSGLMIAEVTSAALMSENKQLSHPASVDSTPTSANQEDHVSMACHGARRLLQMTENLFSIIGIEALAA 445
                                          ************************************************************************** PP

                            TIGR01225 443 aqglefrkaektaaelekvyeavRevveeleeDRvlapDleavkellekesleaaveakvkak 505
                                          +qg+efr++ +t++el+k+++avR v++++eeDR++a+Dl+a+ +l+++++l+aav+a +++k
  lcl|FitnessBrowser__Smeli:SM_b21165 446 VQGIEFRAPLTTSPELQKAAAAVRGVSSSIEEDRYMADDLKAAGDLVASGRLAAAVSAGILPK 508
                                          ********************************************************9998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (506 nodes)
Target sequences:                          1  (511 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: 0.02u 0.02s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 7.78
//
[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