Alignments for a candidate for acn in Halomonas xinjiangensis TRM 0175

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Halomonas xinjiangensis TRM 0175

Align Aconitate hydratase A; ACN; Aconitase; (2R,3S)-2-methylisocitrate dehydratase; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate dehydratase; 2-methyl-cis-aconitate hydratase; Iron-responsive protein-like; IRP-like; RNA-binding protein; EC 4.2.1.3; EC 4.2.1.99 (characterized)
to candidate WP_043529276.1 JH15_RS08095 aconitate hydratase AcnA

Query= SwissProt::Q8ZP52
         (891 letters)



>NCBI__GCF_000759345.1:WP_043529276.1
          Length = 914

 Score = 1243 bits (3217), Expect = 0.0
 Identities = 622/903 (68%), Positives = 724/903 (80%), Gaps = 27/903 (2%)

Query: 12  TLQAKDKTYHYYSLPLAAKSLGDIARLPKSLKVLLENLLRWQDGESVTDEDIQALAGWLK 71
           +L   ++ YHYYSLP AA++LGDI RLP +LK+LLEN LR+ D ESV+ ED+QAL  W +
Sbjct: 12  SLTVGEREYHYYSLPKAAEALGDIQRLPVTLKILLENQLRFADDESVSREDMQALVDWQQ 71

Query: 72  NAHADREIAWRPARVLMQDFTGVPAVVDLAAMREAVKRLGGDTSKVNPLSPVDLVIDHSV 131
            A + REI +RPARVLMQDFTGVP VVDLA+MR AV++LG D S++NPLSPVDLVIDHSV
Sbjct: 72  EARSTREIGYRPARVLMQDFTGVPGVVDLASMRAAVEKLGEDPSRINPLSPVDLVIDHSV 131

Query: 132 TVDHFGDDDAFEENVRLEMERNHERYMFLKWGKQAFSRFSVVPPGTGICHQVNLEYLGKA 191
            VD +GD  AF +NV +EM+RN ERY FL+WG+ AF  F VVPPGTGICHQVNLEYLGK 
Sbjct: 132 MVDKYGDPSAFRDNVAIEMDRNRERYEFLRWGQDAFDNFRVVPPGTGICHQVNLEYLGKT 191

Query: 192 VWSELQDGEWIAYPDSLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQPVSMLIPDVVG 251
           VW + +DG+  AYPD+LVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQPVSMLIP+VVG
Sbjct: 192 VWVKEEDGKSFAYPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQPVSMLIPEVVG 251

Query: 252 FKLTGKLREGITATDLVLTVTQMLRKHGVVGKFVEFYGDGLDSLPLADRATIANMSPEYG 311
           FKLTGKLREGITATDLVLTVTQMLR+ GVVGKFVEFYGDGLD LPLADRATIANM+PEYG
Sbjct: 252 FKLTGKLREGITATDLVLTVTQMLRQKGVVGKFVEFYGDGLDDLPLADRATIANMAPEYG 311

Query: 312 ATCGFFPIDAITLEYMRLSGRSDDLVELVETYAKAQGMWRNPGDEPVFTSTLELDMGDVE 371
           ATCGFFP+D  TL Y+RL+GRSD+ V LVE Y K Q +WR PG EPVF+ TL+LDMGDVE
Sbjct: 312 ATCGFFPVDDETLNYLRLTGRSDEEVALVEAYCKEQDLWRKPGAEPVFSDTLQLDMGDVE 371

Query: 372 ASLAGPKRPQDRVALGDVPKAF-------AASA-------------ELELNTAQR----D 407
           ASLAGPKRPQDRVAL D+   F       AA A             ++ + T +     D
Sbjct: 372 ASLAGPKRPQDRVALSDMKSTFENLMGDDAAEASATARGKFDSEGGQMPVGTHEHFEHHD 431

Query: 408 RQPVDYTMNGQPYQLPDGAVVIAAITSCTNTSNPSVLMAAGLLAKKAVTLGLKRQPWVKA 467
            Q VD  + G  ++L  GAVVIAAITSCTNTSNPSV+MAAGLLA+KAV  GL  +PWVK 
Sbjct: 432 SQDVD--VEGSTFKLNPGAVVIAAITSCTNTSNPSVMMAAGLLARKAVEKGLDTKPWVKT 489

Query: 468 SLAPGSKVVSDYLAQAKLTPYLDELGFNLVGYGCTTCIGNSGPLPEPIETAIKKGDLTVG 527
           SLAPGSKVV+DYLA       L+ LGFNLVGYGCTTCIGNSGPL  PIE AI+ GDLTV 
Sbjct: 490 SLAPGSKVVTDYLAAGGFQDDLNALGFNLVGYGCTTCIGNSGPLLPPIEKAIEDGDLTVA 549

Query: 528 AVLSGNRNFEGRIHPLVKTNWLASPPLVVAYALAGNMNINLATDPLGYDRKGDPVYLKDI 587
           +VLSGNRNFEGR+HPLVKTNWLASPPLVVAYALAGN+ ++++ +PLG  + G PVYL+DI
Sbjct: 550 SVLSGNRNFEGRVHPLVKTNWLASPPLVVAYALAGNVRLDISKEPLGEGKDGKPVYLQDI 609

Query: 588 WPSAQEIARAVELVSSDMFRKEYAEVFEGTEEWKSIQVESSDTYGWQSDSTYIRLSPFFD 647
           WPS  EIA AVE V ++M+RKEYAEVFEG E WK+I V  S  Y W  DSTYI+  PFF+
Sbjct: 610 WPSQAEIAEAVEKVRTEMYRKEYAEVFEGDEVWKAIDVPQSQVYQWSEDSTYIQHPPFFE 669

Query: 648 EMQAQPAPVKDIHGARILAMLGDSVTTDHISPAGSIKPDSPAGRYLQNHGVERKDFNSYG 707
            M  +P P++D+  AR+LAMLGDSVTTDHISPAG+IKPDSPAGRYLQ HGV+  DFNSYG
Sbjct: 670 GMGREPEPLQDVENARVLAMLGDSVTTDHISPAGAIKPDSPAGRYLQEHGVKPMDFNSYG 729

Query: 708 SRRGNHEVMMRGTFANIRIRNEMLPGVEGGMTRHLPGTEAMSIYDAAMLYQQEKTPLAVI 767
           SRRGNHEVMMRGTFAN+RIRNEML GVEGG TRH+P  E M+IYDAAM Y +E  PL VI
Sbjct: 730 SRRGNHEVMMRGTFANVRIRNEMLDGVEGGYTRHVPSDEQMAIYDAAMKYAEEGRPLVVI 789

Query: 768 AGKEYGSGSSRDWAAKGPRLLGIRVVIAESFERIHRSNLIGMGILPLEFPQGVTRKTLGL 827
           AGKEYG+GSSRDWAAKG RLLG+R V+AES+ERIHRSNLIGMG++PL+FP+G  RK+LGL
Sbjct: 790 AGKEYGTGSSRDWAAKGTRLLGVRAVLAESYERIHRSNLIGMGVVPLQFPEGEDRKSLGL 849

Query: 828 TGEEVIDIADLQNLRPGATIPVTLTRSDGSKETVPCRCRIDTATELTYYQNDGILHYVIR 887
           TG+E + I  + +L PG  + VT+ +SD  ++ +   CRIDTA EL YY++ GILHYV+R
Sbjct: 850 TGDEEVSIDGIADLTPGGQVNVTI-KSDKGEKKIEALCRIDTANELEYYRHGGILHYVLR 908

Query: 888 NML 890
            M+
Sbjct: 909 KMI 911


Lambda     K      H
   0.317    0.135    0.401 

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: 2309
Number of extensions: 92
Number of successful extensions: 3
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: 891
Length of database: 914
Length adjustment: 43
Effective length of query: 848
Effective length of database: 871
Effective search space:   738608
Effective search space used:   738608
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: 56 (26.2 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 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