Alignments for a candidate for hutH in Caulobacter crescentus NA1000

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutH in Caulobacter crescentus NA1000

Align Histidine ammonia-lyase (EC 4.3.1.3) (characterized)
to candidate CCNA_01010 CCNA_01010 histidine ammonia-lyase

Query= reanno::Korea:Ga0059261_3963
         (497 letters)



>FitnessBrowser__Caulo:CCNA_01010
          Length = 513

 Score =  714 bits (1844), Expect = 0.0
 Identities = 371/491 (75%), Positives = 407/491 (82%), Gaps = 5/491 (1%)

Query: 1   MITPGYTPLSTWNAIYRGEAAPLDPSCRDKIQASADAVEAILARHEPVYGINTGFGKLAS 60
           ++ PG  PL+ W AIYRG +A L  S    I  SA AV+ ILA+ EPVYGINTGFGKLAS
Sbjct: 9   VLNPGAVPLAEWKAIYRGASARLAESAWPVIAESAAAVQRILAKGEPVYGINTGFGKLAS 68

Query: 61  VRIGDEDLETLQRNIVLSHAAGVGAPMPAPVVRLMIALKLASLAQGHSGVRPATIAMLQD 120
           VRIGD DLETLQRNIVLSHAAGVG P P PV+RLM+ALKLASLAQG SGVR  T+ ML++
Sbjct: 69  VRIGDADLETLQRNIVLSHAAGVGEPSPVPVIRLMMALKLASLAQGASGVRVETVRMLEE 128

Query: 121 MLDRGITPIIPSQGSVGASGDLAPLAHLAAAMIGTGEVLVDGVVRPARDVLA-----PLT 175
           ML  G+TP++P QGSVGASGDLAPL+H+AA MIG GE+ V G   PA   LA     PLT
Sbjct: 129 MLVEGLTPVVPCQGSVGASGDLAPLSHMAATMIGVGEIFVGGQRLPAAQALAQAGLEPLT 188

Query: 176 LGPKEGLALLNGTQFSTAYALAALFETERLFRAALVTGALSTEAAKGSDTPFDPRIHQVR 235
           LGPKEGLALLNGTQFSTA ALA LFE ERLF++ALVTGALSTEAAKGSDTPFDPRIH +R
Sbjct: 189 LGPKEGLALLNGTQFSTANALAGLFEAERLFQSALVTGALSTEAAKGSDTPFDPRIHTLR 248

Query: 236 GHRGQIEVADALAGLMSGSAIRASHREGDERVQDPYCLRCQPQVMGACLDLIRQAAATLA 295
            H GQIE A AL  LMS S IRASH + DERVQDPYCLRCQPQVMGA LD++RQAA TLA
Sbjct: 249 RHVGQIETAAALRALMSASEIRASHLKEDERVQDPYCLRCQPQVMGAALDILRQAATTLA 308

Query: 296 IEANGVTDNPLIFPDTGEALSGGNFHAEPVAFAADMLAMALCEIGSLSERRIAMLVDPAL 355
            EAN V+DNPLIFP+  EALSGGNFHAEPVAFAADM+A+A+CEIGS++ERRIAMLVDPAL
Sbjct: 309 TEANCVSDNPLIFPEADEALSGGNFHAEPVAFAADMIALAVCEIGSIAERRIAMLVDPAL 368

Query: 356 SGLPAFLTPRPGLNSGFMIPQVTAAALVSENKQRAHPASVDSIPTSANQEDHVSMAGHGA 415
           SGLPAFLTP+PGLNSGFMIPQVTAAALVSENKQRA+PASVDSIPTSANQEDHVSMA HGA
Sbjct: 369 SGLPAFLTPKPGLNSGFMIPQVTAAALVSENKQRAYPASVDSIPTSANQEDHVSMAAHGA 428

Query: 416 RRLMEMAANLANVLGIEYLAAAQGCDFHAPLTSSEPLEAARSLLRNQVPHLEDDRHFAPD 475
           RRL+ M  N   VLGIE LAAAQGCDFHAPL SS  LEA R+L R++VPHL DDRHF PD
Sbjct: 429 RRLLAMVENADAVLGIELLAAAQGCDFHAPLRSSAALEAVRALTRSKVPHLSDDRHFHPD 488

Query: 476 MAAATALVAGG 486
           M AA  LV  G
Sbjct: 489 MEAANTLVRSG 499


Lambda     K      H
   0.319    0.134    0.388 

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: 802
Number of extensions: 30
Number of successful extensions: 2
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: 497
Length of database: 513
Length adjustment: 34
Effective length of query: 463
Effective length of database: 479
Effective search space:   221777
Effective search space used:   221777
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 (21.7 bits)
S2: 52 (24.6 bits)

Align candidate CCNA_01010 CCNA_01010 (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.28791.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.4e-210  686.0   6.5   1.7e-210  685.7   6.5    1.0  1  lcl|FitnessBrowser__Caulo:CCNA_01010  CCNA_01010 histidine ammonia-lya


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Caulo:CCNA_01010  CCNA_01010 histidine ammonia-lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  685.7   6.5  1.7e-210  1.7e-210       2     498 ..       9     505 ..       8     509 .. 0.99

  Alignments for each domain:
  == domain 1  score: 685.7 bits;  conditional E-value: 1.7e-210
                             TIGR01225   2 vldgesltledleavarekarvelsaaaeeavaksravieeivaedktvYGvntGFGklasvkidkedlaeLq 74 
                                           vl+++ + l++ +a++r +a ++l+++a   +a+s+a++++i+a+ ++vYG+ntGFGklasv+i  +dl++Lq
  lcl|FitnessBrowser__Caulo:CCNA_01010   9 VLNPGAVPLAEWKAIYR-GASARLAESAWPVIAESAAAVQRILAKGEPVYGINTGFGKLASVRIGDADLETLQ 80 
                                           68888999999999987.5789*************************************************** PP

                             TIGR01225  75 rnlvrsHaaGvGepleeevvRallvlrlnslakGysgvraevlellvallnaevlPvvpekGsvGasGDLAPL 147
                                           rn+v+sHaaGvGep +  v+R++++l+l sla+G+sgvr+e++++l ++l ++ +Pvvp +GsvGasGDLAPL
  lcl|FitnessBrowser__Caulo:CCNA_01010  81 RNIVLSHAAGVGEPSPVPVIRLMMALKLASLAQGASGVRVETVRMLEEMLVEGLTPVVPCQGSVGASGDLAPL 153
                                           ************************************************************************* PP

                             TIGR01225 148 ahlalvliGeGeaefegevmdaaeaLaaaglePvtlkakEGlALinGtqlmtalavlalvdaekllesadiaa 220
                                           +h+a+++iG Ge+++ g++++aa+aLa+agleP+tl  kEGlAL+nGtq++ta a+++l++ae+l +sa +++
  lcl|FitnessBrowser__Caulo:CCNA_01010 154 SHMAATMIGVGEIFVGGQRLPAAQALAQAGLEPLTLGPKEGLALLNGTQFSTANALAGLFEAERLFQSALVTG 226
                                           ************************************************************************* PP

                             TIGR01225 221 alsleallgtskafdpdihevrphrgqiavaarlrellagseiaeshk.dedrvqDaYslRciPqvhGavldt 292
                                           als+ea++g++++fdp+ih++r h gqi++aa+lr l++ sei+ sh  +++rvqD+Y+lRc+Pqv+Ga+ld 
  lcl|FitnessBrowser__Caulo:CCNA_01010 227 ALSTEAAKGSDTPFDPRIHTLRRHVGQIETAAALRALMSASEIRASHLkEDERVQDPYCLRCQPQVMGAALDI 299
                                           ***********************************************9899********************** PP

                             TIGR01225 293 ldqvkevlaiElnsatDnPlvfadegevvsgGnFHgepvAlaldflaiaiaelgaiseRRierlldpalseLp 365
                                           l+q++++la+E+n ++DnPl+f++ +e  sgGnFH+epvA+a+d++a+a++e+g+i+eRRi+ l+dpals+Lp
  lcl|FitnessBrowser__Caulo:CCNA_01010 300 LRQAATTLATEANCVSDNPLIFPEADEALSGGNFHAEPVAFAADMIALAVCEIGSIAERRIAMLVDPALSGLP 372
                                           ************************************************************************* PP

                             TIGR01225 366 pFLaedsGlnsGlmiaqytaAaLvsenkaLahPasvDsiptsanqEDHvsmgaaaarkllevvenvrrviaiE 438
                                           +FL++++GlnsG+mi+q+taAaLvsenk+ a+PasvDsiptsanqEDHvsm+a++ar+ll +ven+  v++iE
  lcl|FitnessBrowser__Caulo:CCNA_01010 373 AFLTPKPGLNSGFMIPQVTAAALVSENKQRAYPASVDSIPTSANQEDHVSMAAHGARRLLAMVENADAVLGIE 445
                                           ************************************************************************* PP

                             TIGR01225 439 llaaaqglefrkaektaaelekvyeavRevveeleeDRvlapDleavkellekesleaav 498
                                           llaaaqg +f+++ +++a+le+v+++ R++v++l++DR + pD+ea+++l++++ ++aav
  lcl|FitnessBrowser__Caulo:CCNA_01010 446 LLAAAQGCDFHAPLRSSAALEAVRALTRSKVPHLSDDRHFHPDMEAANTLVRSGAVIAAV 505
                                           ********************************************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (506 nodes)
Target sequences:                          1  (513 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 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 9.42
//
[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