Alignments for a candidate for hutH in Halomonas desiderata SP1

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutH in Halomonas desiderata SP1

Align Histidine ammonia-lyase (EC 4.3.1.3) (characterized)
to candidate WP_086509677.1 BZY95_RS09375 histidine ammonia-lyase

Query= reanno::pseudo5_N2C3_1:AO356_09605
         (507 letters)



>NCBI__GCF_002151265.1:WP_086509677.1
          Length = 527

 Score =  575 bits (1482), Expect = e-168
 Identities = 295/492 (59%), Positives = 368/492 (74%)

Query: 4   AEKIVITGAPLRWQDVVAVARFGAELELSTQTWARIDNAQAIVQRIVESGERAYGVNTGL 63
           AE+IV+  AP+ WQ VV VAR GA L L+   W RI  A+  V++I  S    YG+NTGL
Sbjct: 5   AERIVLGAAPVEWQQVVRVARHGALLSLTKAAWKRIAAARQAVEKIAASTVPHYGINTGL 64

Query: 64  GALCNVSLKDEQLSQLSRNTLLSHACGVGAPLTDEQTRAILCAAILNYSQGKSGIHRRVV 123
           GALCNV+L+ ++L +LS +TL+SHACGVGAPL  EQ RAI+C A++NYS G SGI   VV
Sbjct: 65  GALCNVALERDELQRLSHHTLMSHACGVGAPLRTEQVRAIICCAVINYSHGYSGISPAVV 124

Query: 124 EALLALLNRGITPQVPSQGSVGYLTHMAHIGIALLGVGQVSYRGQIVPAQQALVAEGLQP 183
           + LL LLN  +TP VPS+GSVGYLTHMAHIG+AL+G G+V + GQ +PA+QAL A G+ P
Sbjct: 125 KGLLHLLNEQVTPIVPSRGSVGYLTHMAHIGLALIGHGEVEFDGQRMPARQALDAIGMPP 184

Query: 184 VQLGAKDGLCLVNGTPCMTGLSCLALADATRLVQWADVIGAMSFEAQRGQIAAFDAEIIA 243
           + LG KDGL LVNGTP MTGL+CLAL D  RL  WAD++GAMSFEA  GQ  A   ++ +
Sbjct: 185 LTLGPKDGLSLVNGTPAMTGLACLALEDVARLAAWADIVGAMSFEALGGQWDALLPQVTS 244

Query: 244 LKPHPGMQQVGVNLRALLDGSEVIAASRGIRTQDALSIRSIPQVHGAARDQLAHARQQIE 303
           LK H G+Q  G NLR LL GS  +A  +G   QDALS+RSIPQVHGA RDQ AHA +QI+
Sbjct: 245 LKRHQGVQHTGDNLRRLLQGSRRLARCQGQHLQDALSLRSIPQVHGACRDQFAHAARQID 304

Query: 304 TELNAVTDNPLLLGTPENFRVMSQANPHGQSVALAADLLAIAMAEIGSIAERRLDRLINP 363
            EL++ TDNPL++ T E++R++S ANPHG SVA+A DLLAIA+ E  SI+ERR  RL+ P
Sbjct: 305 HELDSATDNPLVVATEESYRIISNANPHGASVAMACDLLAIAVCEWSSISERRTYRLVTP 364

Query: 364 HVSGLPAFLVANPGVNSGMMIVQYVAASLCAENKQLAQPAVLDNFVTSGLQEDHLSMGTN 423
             S LP FL  + GV SGMMI QY AASL A+NK+LAQPAV+DNF+TSGLQEDHLS+G +
Sbjct: 365 QASRLPPFLSNDVGVKSGMMIAQYTAASLVADNKRLAQPAVVDNFLTSGLQEDHLSLGES 424

Query: 424 AALKLHRALENCTQILAIEYLLAAQAFEFLKAQRFGAGTDIAWKLLRERVPPYDQDRWLA 483
           AALKL +AL+N  Q+LAIEYLLAAQAF+ +  Q F  GT++AWK LRE +P YD++  L 
Sbjct: 425 AALKLDQALDNAFQVLAIEYLLAAQAFDLIDDQNFAPGTELAWKALREVIPFYDEEHPLH 484

Query: 484 PDIASAAGLLKD 495
            D+ +A  LL+D
Sbjct: 485 QDLQTARHLLRD 496


Lambda     K      H
   0.320    0.133    0.385 

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: 758
Number of extensions: 23
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: 507
Length of database: 527
Length adjustment: 35
Effective length of query: 472
Effective length of database: 492
Effective search space:   232224
Effective search space used:   232224
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: 52 (24.6 bits)

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

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
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 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