Alignments for a candidate for hutH in Collimonas arenae Ter10

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutH in Collimonas arenae Ter10

Align Histidine ammonia-lyase (EC 4.3.1.3) (characterized)
to candidate WP_061533210.1 CAter10_RS09455 histidine ammonia-lyase

Query= reanno::BFirm:BPHYT_RS07555
         (506 letters)



>NCBI__GCF_001584165.1:WP_061533210.1
          Length = 512

 Score =  602 bits (1552), Expect = e-176
 Identities = 310/496 (62%), Positives = 385/496 (77%), Gaps = 1/496 (0%)

Query: 1   MTLKPGYLTLPQLRQIAREHVALQLDPASHAAIDACAQAVADIAAKGEPAYGINTGFGRL 60
           +TL+PG ++L ++R I  + V LQL  +++ AI+A A  VA I  +G+ AYGINTGFG+L
Sbjct: 5   LTLQPGKMSLAEIRSIWADAVPLQLPASAYTAINASAATVARIVERGDAAYGINTGFGKL 64

Query: 61  ASTHIPHDQLELLQRNLVLSHAVGVGEPMSRPVVRLLIALKLSSLGRGHSGIRREVMEAL 120
           A T IP +QLELLQRNL+LSH+VG G+ M    VRL++A+K+ SL RG SGIR +V++ L
Sbjct: 65  AKTRIPDEQLELLQRNLILSHSVGTGDLMDDAAVRLILAMKIGSLARGFSGIRAQVIDTL 124

Query: 121 ITLYNADVLPVIPVKGSVGASGDLAPLAHMSATLLGVGEVFAKGERMPATEGLALVGLKP 180
           + +YNA ++P IPVKGSVGASGDLAPL+HM+  +LG G+V   G+ + A E LA  G+ P
Sbjct: 125 LAIYNAGIMPCIPVKGSVGASGDLAPLSHMTLAILGEGQVRVDGKLVDAKEALAKAGIAP 184

Query: 181 LTLQAKEGLALLNGTQASTALALYNMFAIEDLYRTALVSGALSVDAAMGSVKPFDARIHE 240
           + L AKEGLAL+NGTQ STAL L+ +F  E +   A V+GAL+VDAA GS  PFD R+HE
Sbjct: 185 IVLAAKEGLALINGTQVSTALTLHGLFLAERVLEAAAVTGALAVDAARGSDAPFDPRVHE 244

Query: 241 LRGHQGQIDAAGAYRSLLQGSGINVSH-ADCDKVQDPYSLRCQPQVMGACLDQMRHAANV 299
           +RG  GQI  A  YR LL GS I  SH  + ++VQDPYSLRCQPQVMGAC+D + +AA  
Sbjct: 245 VRGQPGQIATAKIYRQLLNGSAIRQSHLVNDERVQDPYSLRCQPQVMGACVDLIGNAART 304

Query: 300 LLLEANAVSDNPLIFPDTGEVLSGGNFHAEPVAFAADNLALAAAEIGALAERRIALLIDA 359
           LL+EANAV+DNPLI+ +  EV+SGGNFHAEPVAFAAD LALA AEIGAL+ERRIALLID+
Sbjct: 305 LLIEANAVTDNPLIYAEHDEVISGGNFHAEPVAFAADTLALAIAEIGALSERRIALLIDS 364

Query: 360 TLSGLPPFLVRDGGVNSGFMIAHVTAAALASENKTLAHPASVDSLPTSANQEDHVSMATF 419
           +LSGLPPFLV+  G+NSGFMIAHVTAAALASENK+LAHPASVDSLPTSANQEDHVSMATF
Sbjct: 365 SLSGLPPFLVQSSGLNSGFMIAHVTAAALASENKSLAHPASVDSLPTSANQEDHVSMATF 424

Query: 420 AARKLGDIAENTANILSIELLAAAQGVDLRAPHKTSPSLQKVMDAVRKDVAHYELDHYFA 479
           A R+L ++A NTA I++IELLAAAQGVD   P  TSP L  V+  +R+ VA Y+ D +FA
Sbjct: 425 AGRRLHEMAHNTATIVAIELLAAAQGVDCHQPLTTSPLLADVLQRLRQQVAFYDKDRFFA 484

Query: 480 PDIAAVTRLVQDGTIA 495
           PDI A  +LV  GT++
Sbjct: 485 PDIEAAKQLVLQGTVS 500


Lambda     K      H
   0.318    0.133    0.374 

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: 663
Number of extensions: 23
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: 506
Length of database: 512
Length adjustment: 34
Effective length of query: 472
Effective length of database: 478
Effective search space:   225616
Effective search space used:   225616
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 WP_061533210.1 CAter10_RS09455 (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.2253948.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.3e-211  689.4   9.8   1.5e-211  689.1   9.8    1.0  1  NCBI__GCF_001584165.1:WP_061533210.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001584165.1:WP_061533210.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  689.1   9.8  1.5e-211  1.5e-211       2     498 ..       6     503 ..       5     509 .. 0.99

  Alignments for each domain:
  == domain 1  score: 689.1 bits;  conditional E-value: 1.5e-211
                             TIGR01225   2 vldgesltledleavarekarvelsaaaeeavaksravieeivaedktvYGvntGFGklasvkidkedlaeLq 74 
                                           +l++++++l++++++ ++  +++l a+a  a+++s+a++++iv+   + YG+ntGFGkla+++i  e+l+ Lq
  NCBI__GCF_001584165.1:WP_061533210.1   6 TLQPGKMSLAEIRSIWADAVPLQLPASAYTAINASAATVARIVERGDAAYGINTGFGKLAKTRIPDEQLELLQ 78 
                                           789999******************************************************************* PP

                             TIGR01225  75 rnlvrsHaaGvGepleeevvRallvlrlnslakGysgvraevlellvallnaevlPvvpekGsvGasGDLAPL 147
                                           rnl++sH++G G+ +++++vR++l++++ sla+G+sg+ra+v+++l+a+ na+++P +p kGsvGasGDLAPL
  NCBI__GCF_001584165.1:WP_061533210.1  79 RNLILSHSVGTGDLMDDAAVRLILAMKIGSLARGFSGIRAQVIDTLLAIYNAGIMPCIPVKGSVGASGDLAPL 151
                                           ************************************************************************* PP

                             TIGR01225 148 ahlalvliGeGeaefegevmdaaeaLaaaglePvtlkakEGlALinGtqlmtalavlalvdaekllesadiaa 220
                                           +h++l+++GeG+++++g+++da+eaLa+ag++P+ l+akEGlALinGtq++tal++ +l+ ae++le+a +++
  NCBI__GCF_001584165.1:WP_061533210.1 152 SHMTLAILGEGQVRVDGKLVDAKEALAKAGIAPIVLAAKEGLALINGTQVSTALTLHGLFLAERVLEAAAVTG 224
                                           ************************************************************************* PP

                             TIGR01225 221 alsleallgtskafdpdihevrphrgqiavaarlrellagseiaeshk.dedrvqDaYslRciPqvhGavldt 292
                                           al+++a+ g++++fdp++hevr+++gqia+a+  r+ll+gs i++sh  +++rvqD+YslRc+Pqv+Ga+ d 
  NCBI__GCF_001584165.1:WP_061533210.1 225 ALAVDAARGSDAPFDPRVHEVRGQPGQIATAKIYRQLLNGSAIRQSHLvNDERVQDPYSLRCQPQVMGACVDL 297
                                           ************************************************9************************ PP

                             TIGR01225 293 ldqvkevlaiElnsatDnPlvfadegevvsgGnFHgepvAlaldflaiaiaelgaiseRRierlldpalseLp 365
                                           + +++++l iE+n++tDnPl++a+++ev+sgGnFH+epvA+a+d+la+aiae+ga+seRRi++l+d +ls+Lp
  NCBI__GCF_001584165.1:WP_061533210.1 298 IGNAARTLLIEANAVTDNPLIYAEHDEVISGGNFHAEPVAFAADTLALAIAEIGALSERRIALLIDSSLSGLP 370
                                           ************************************************************************* PP

                             TIGR01225 366 pFLaedsGlnsGlmiaqytaAaLvsenkaLahPasvDsiptsanqEDHvsmgaaaarkllevvenvrrviaiE 438
                                           pFL++ sGlnsG+mia++taAaL+senk+LahPasvDs+ptsanqEDHvsm++ a+r+l e+++n+++++aiE
  NCBI__GCF_001584165.1:WP_061533210.1 371 PFLVQSSGLNSGFMIAHVTAAALASENKSLAHPASVDSLPTSANQEDHVSMATFAGRRLHEMAHNTATIVAIE 443
                                           ************************************************************************* PP

                             TIGR01225 439 llaaaqglefrkaektaaelekvyeavRevveeleeDRvlapDleavkellekesleaav 498
                                           llaaaqg++ +++ +t++ l+ v + +R++v+ +++DR++apD+ea+k+l+ ++++ a  
  NCBI__GCF_001584165.1:WP_061533210.1 444 LLAAAQGVDCHQPLTTSPLLADVLQRLRQQVAFYDKDRFFAPDIEAAKQLVLQGTVSASC 503
                                           ****************************************************99987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (506 nodes)
Target sequences:                          1  (512 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: 16.97
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
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Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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 2024 update 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