Alignments for a candidate for acn in Thermophagus xiamenensis HS1

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Thermophagus xiamenensis HS1

Align Aconitate hydratase A; ACN; Aconitase; EC 4.2.1.3; (2R,3S)-2-methylisocitrate dehydratase; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate dehydratase; Iron-responsive protein-like; IRP-like; Probable 2-methyl-cis-aconitate hydratase; EC 4.2.1.99; RNA-binding protein (uncharacterized)
to candidate WP_010527966.1 GQW_RS0110835 aconitate hydratase

Query= curated2:Q2A1K3
         (937 letters)



>NCBI__GCF_000220155.1:WP_010527966.1
          Length = 754

 Score =  252 bits (644), Expect = 6e-71
 Identities = 251/813 (30%), Positives = 349/813 (42%), Gaps = 153/813 (18%)

Query: 64  HKVLDWDAKASSRPE--IPHMPARVVMQDFTGVPAVVDLAAMRKAIKDAGGDADKINPLV 121
           H   D+ +K   R +  +   P RV MQD T   A++      K         DK+   V
Sbjct: 40  HLADDFPSKPYERGKDYVNFSPDRVAMQDATAQMALLQFMQAGK---------DKV--AV 88

Query: 122 DTAMVIDHSVQVDFYGT---KTALAQN--VAKEFERNGERYSLLKWAQKAFDDFIVVPPG 176
            + +  DH +Q         KTA   N  V         +Y L  W            PG
Sbjct: 89  PSTVHADHLIQAKIGAEDDLKTAQVTNKEVYDFLSSVCNKYGLGFWK-----------PG 137

Query: 177 MGIIHQVNLEYLAKDALVKNINGEDVIYPD-TLVGTDSHTTMINGVGAVGWGVGGIEAEA 235
            GIIHQV LE  A              +P   ++GTDSHT    G+G +  GVGG +A  
Sbjct: 138 AGIIHQVVLENYA--------------FPGGMMIGTDSHTPNAGGLGMIAIGVGGADAVD 183

Query: 236 VMLGQPYYMVLPDVVGVKFTGKLKTGVTATDLVLKVTEVLRKHGVVGKFVEYYGEGLESL 295
           VM G P+ +  P ++GVK TGKL       D++LKV  +L   G  G  +EY+GEG  SL
Sbjct: 184 VMAGMPWELKFPKLIGVKLTGKLNGWTAPKDIILKVAGLLTVKGGTGYILEYFGEGARSL 243

Query: 296 SLPDRATIANMTPEYGATIGFFPVDEVTLDFFNNTNRSELVDAAREMYKEQLLFRENPAE 355
           S   + TI NM  E GAT   F  DE    +   TNR ++ DAA ++ KE L       E
Sbjct: 244 SATGKGTIGNMGAEIGATTSTFGYDEAMERYLRATNRDDVADAANQI-KELLTGDPETYE 302

Query: 356 EPE--YSNIVEIDLSEVESNLAGPKRPQDRVAFHDMKKAFAEALVHEQGLHGFGLTDEQL 413
            PE  +  ++EI+LSE+E ++ GP  P        M+                    E+ 
Sbjct: 303 HPEKYFDQVIEINLSELEPHINGPFTPDRATPISKMR--------------------EEA 342

Query: 414 QKSAEVKGLNERITHGSVAIAAITSCTNTSNPSLLLGAGLLAKKANEKGLKVKPFVKTSL 473
           QK+              V +  I SCTN+S   +   A  +AK+A EKGLKVK   + ++
Sbjct: 343 QKNG---------WPTKVEVGLIGSCTNSSYEDISRAAS-IAKQALEKGLKVKS--EFTV 390

Query: 474 APGSQVVTQYLEKANLLPELENLGFNLVGYGCTTCIGNSGPLDEPVVEAINEADLIVAS- 532
            PGS+ V   +E+   +   E +G  +    C  CIG         + A   AD    + 
Sbjct: 391 TPGSEQVRYTIERDGFIDLFEKIGGKVFANACGPCIG---------MWARENADKQEKNT 441

Query: 533 -VSSGNRNFEGRI--NPHIKANYLASPIHVVAYALAGTVDFDPVEDAIGKDAEGNDVYLA 589
            V S NRNF  R   NP+  A ++ASP  V A A++G + F+P+ D +  D +G +V L 
Sbjct: 442 IVHSFNRNFAKRADGNPNTHA-FVASPEVVTAIAISGELGFNPLTDTLIND-KGEEVKLD 499

Query: 590 DIWPTTEEIAAIQSHVINSDMFKKAYATVLDGTEEWQKLKAPEGKLYEFDSSSTYIQCPN 649
              PT  E+              K +    +G +E  K  +    + + DS    +  P 
Sbjct: 500 P--PTGFELP------------PKGFDVKENGYQEPAKDGSKVEVVVKPDSERLQLLTP- 544

Query: 650 FFEKFAEGNDDLDIKGARTLLMLGDSVTTDHISPAGAIPEEYPAGQYLKSHGVEKKDFNS 709
            FE +    D  +I GA+ L+      TTDHIS AG      P  +Y             
Sbjct: 545 -FEPW----DGKNIMGAKLLIKAEGKCTTDHISMAG------PWLRY------------- 580

Query: 710 YGSRRGNHEVMMRGTFANIRIRNLLLD-----NVEGGFTKYHLDGSQQYVFDAAMKYKEK 764
                       RG   NI   NLL+      N E    K  L G    V D    YK K
Sbjct: 581 ------------RGHLDNIS-NNLLIGAVNAFNHETNNVKNQLTGEYGKVPDVQRAYKAK 627

Query: 765 GIPLVILAGKEYGTGSSRDWAAKGTFLLGVKAVIAESYERIHRSNLVGMGVLPLEYVNGQ 824
           GIP V++    YG GSSR+ AA     LGVK ++ +S+ RIH +NL   G+L L + N  
Sbjct: 628 GIPTVVVGDHNYGEGSSREHAAMEPRHLGVKVILVKSFARIHETNLKKQGMLALTFQNEN 687

Query: 825 NAKTLGLDGTEMFNIKNLNNIKPRQIVIVEAVH 857
           +   +  D T  FN  +L    P + V +E VH
Sbjct: 688 DYDKILEDDT--FNFIDLEQFSPNKPVTIEVVH 718


Lambda     K      H
   0.315    0.134    0.384 

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: 1512
Number of extensions: 72
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 937
Length of database: 754
Length adjustment: 42
Effective length of query: 895
Effective length of database: 712
Effective search space:   637240
Effective search space used:   637240
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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Protein sequences (fasta format)
Organisms (tab-delimited)
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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