GapMind for catabolism of small carbon sources

 

Aligments for a candidate for hutH in Shewanella loihica PV-4

Align Histidine ammonia-lyase; Histidase; EC 4.3.1.3 (uncharacterized)
to candidate 5209827 Shew_2280 phenylalanine/histidine ammonia-lyase (RefSeq)

Query= curated2:Q73Q56
         (507 letters)



>lcl|FitnessBrowser__PV4:5209827 Shew_2280 phenylalanine/histidine
           ammonia-lyase (RefSeq)
          Length = 552

 Score =  204 bits (518), Expect = 9e-57
 Identities = 159/523 (30%), Positives = 244/523 (46%), Gaps = 40/523 (7%)

Query: 6   VTVTGSSLTIEDVVAVARHGAEVKLSADAKKRIKDSKKIVDDIVKSGKPTYGISTGFGEL 65
           V + G  LT     A+A  GA+V ++  A   +  +  ++ +  + GKP YG++ G G L
Sbjct: 32  VVLDGQHLTQAQAWAIA-DGAKVDIAPQAASALVKAHDLLMEAARLGKPVYGLTVGVG-L 89

Query: 66  STVTITKDQNGALQRNLILS-----------HACGVGNPFPEDIVRAIMLLRLNTHASGF 114
           +      D NG L   ++ +           H+ GVG P P  + R  + +RLNT  SG 
Sbjct: 90  NKDHKLFDANGELSAEVMAASKSFNYSTLRAHSAGVGEPMPVRLTRVALAVRLNTILSGH 149

Query: 115 SGVTPSVPDILVDMLNKGVIPYVPEKGSLGASGDLANLAHIALVMIGEGKAYYEGKLMEG 174
           +GV P V +I    LN+G+ P +P  G++G + D+   +H+ L MIGE   +Y+GK M  
Sbjct: 150 TGVQPYVAEIYQAYLNQGITPVIPSLGTVGEA-DILLASHVGLAMIGEWDVFYQGKRMSS 208

Query: 175 KAALAKAGLKPVVLSGKDGLGIINGTPVMSGIGALALHDAEQLLKAANMGASLVFEAFRG 234
             A++KAG+KP+   GKD L I++   V          DAE LL+ +     L  E   G
Sbjct: 209 VEAMSKAGVKPLKPIGKDALSILSNNSVAVAYAMQGYQDAEHLLEVSPTVFGLSLEGLNG 268

Query: 235 ITAALDPRIHKSRPHKGQIDTAAFILKMLKGSS--SINTRENDVQDPYTLRCVPQVHGAS 292
             A   P+ +  RP      T   IL  L GS    +N+ E  +QDP + R       ++
Sbjct: 269 NVAPFLPQTNDIRPFPYLKATTEDILGSLSGSYLWDLNS-ERPLQDPLSYRTTAYTLASA 327

Query: 293 ADAIAYVRKVLEIEINAVTDNPLV-------FPDNHDVI------SGG-----NFHGQPI 334
             A++ + +V++I+IN   DNP V       + +N  V        GG     NF   P+
Sbjct: 328 QKALSDLGQVIDIQINHSDDNPGVILGASKQYAENSQVAKYLVEGKGGVFPTTNFEPLPV 387

Query: 335 AITMDFLGIAVSELANISERRIERLVNPQLNGGLPAFLIENGGVNSGFMIPQYTAASLVS 394
           A+ +  L +A++ +++ S  R   L +      LP FL   G     F   Q T   +  
Sbjct: 388 ALAVQQLSVALTHVSHNSAMRTIHLSDDHFT-HLPRFLSAPGNNGHAFGAIQKTFVDMQV 446

Query: 395 ENKVLAHPASVDSITSSGNKEDHVSMGTTAARKITEIVKNVRHVLAIEWLTAAQACDLRG 454
            NK+LA P S D I  +GN ED  +    A+  + +IV N+  +  +E L + QA DLR 
Sbjct: 447 RNKMLATPVSFDGIQIAGNIEDTFTNLKLASDNLIQIVDNINTMYGLELLHSTQAIDLRK 506

Query: 455 VK----KYGKGTGEMMKLIRKHISKVTEDRILYNDIMKALEII 493
                 K GK T  M +  R+ +  V  DR    DI  + + I
Sbjct: 507 AANADLKLGKATQAMYQAYRQQVPFVELDRPFTPDIQASHDFI 549


Lambda     K      H
   0.316    0.134    0.375 

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: 559
Number of extensions: 27
Number of successful extensions: 7
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: 507
Length of database: 552
Length adjustment: 35
Effective length of query: 472
Effective length of database: 517
Effective search space:   244024
Effective search space used:   244024
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 (21.6 bits)
S2: 52 (24.6 bits)

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:

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:

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:

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, or view the source code.

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