Alignments for a candidate for acn in Allochromatium vinosum DSM 180

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Allochromatium vinosum DSM 180

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_012970720.1 ALVIN_RS07480 aconitate hydratase AcnA

Query= SwissProt::Q8ZP52
         (891 letters)



>NCBI__GCF_000025485.1:WP_012970720.1
          Length = 887

 Score = 1073 bits (2775), Expect = 0.0
 Identities = 550/888 (61%), Positives = 656/888 (73%), Gaps = 16/888 (1%)

Query: 9   SKDTLQAKDKTYHYYSLPLAAKSLGDIARLPKSLKVLLENLLRWQDGESVTDEDIQALAG 68
           +K TL    + Y  + L     S    ARLP S+K+LLENLLR +DG +VT EDI+  + 
Sbjct: 7   AKSTLNVAGQEYEIFKLDAVPNS----ARLPFSIKILLENLLRNEDGVTVTREDIEYFSN 62

Query: 69  WLKNAHADREIAWRPARVLMQDFTGVPAVVDLAAMREAVKRLGGDTSKVNPLSPVDLVID 128
           W   A  D+EI +RPARVLMQDFTGVPAVVDLAAMR+A++ LGGD +++NPL P +LVID
Sbjct: 63  WNPQAEPDKEIQYRPARVLMQDFTGVPAVVDLAAMRDAMRALGGDPTRINPLQPAELVID 122

Query: 129 HSVTVDHFGDDDAFEENVRLEMERNHERYMFLKWGKQAFSRFSVVPPGTGICHQVNLEYL 188
           HSV VDHFG D AF  N  LE +RN ERY FLKWG+QAF  F VVPP TGI HQVN+EYL
Sbjct: 123 HSVQVDHFGSDGAFALNAELEFQRNQERYKFLKWGQQAFDGFKVVPPDTGIVHQVNVEYL 182

Query: 189 GKAVWSELQDGEWIAYPDSLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQPVSMLIPD 248
            + V+ +  DG   AY D+ VGTDSHTTM+NG+GVLGWGVGGIEAEA+MLGQPVSML+P 
Sbjct: 183 ARVVFPKPVDGTTQAYFDTCVGTDSHTTMVNGIGVLGWGVGGIEAEASMLGQPVSMLVPK 242

Query: 249 VVGFKLTGKLREGITATDLVLTVTQMLRKHGVVGKFVEFYGDGLDSLPLADRATIANMSP 308
           VVGFKLTG L+EG+TATDLVLT+ + LRKHGVVGKFVEFYG  + SLP+ +R TIANM P
Sbjct: 243 VVGFKLTGTLKEGVTATDLVLTIVEQLRKHGVVGKFVEFYGPAIASLPMGERNTIANMGP 302

Query: 309 EYGATCGFFPIDAITLEYMRLSGRSDDLVELVETYAKAQGMWRN-PGDEPVFTSTLELDM 367
           EYGATCG FPID +TL+Y+RL+GR +  + LVE Y KAQG+W      E  ++ TLELD+
Sbjct: 303 EYGATCGLFPIDQVTLDYLRLTGRDEAQIALVEAYCKAQGVWHTADAPEAEYSETLELDL 362

Query: 368 GDVEASLAGPKRPQDRVALGDV----PKAFAA-SAELELNTAQRDRQPVDYTMNGQPYQL 422
           GDV  SLAGPKRPQDRVAL D+    PKA AA  AE  L T    +  +D    GQ  ++
Sbjct: 363 GDVAPSLAGPKRPQDRVALTDMASHFPKALAALKAERNLPTKGAAKAVID----GQEVEI 418

Query: 423 PDGAVVIAAITSCTNTSNPSVLMAAGLLAKKAVTLGLKRQPWVKASLAPGSKVVSDYLAQ 482
            DG++V+AAITSCTNTSNPSVL+ AGL+AKKAV LGLKR PWVK +  PGS  V+ YL +
Sbjct: 419 SDGSIVVAAITSCTNTSNPSVLIGAGLVAKKAVALGLKRAPWVKTAFGPGSMAVTRYLDR 478

Query: 483 AKLTPYLDELGFNLVGYGCTTCIGNSGPLPEPIETAIKKGDLTVGAVLSGNRNFEGRIHP 542
           A LT  L  LGF+ VGYGCT CIGN+GPLPEP+  AI   +L   ++LSGNRNFEGR+H 
Sbjct: 479 AGLTEPLKALGFHNVGYGCTVCIGNTGPLPEPVSKAIADNELCAVSILSGNRNFEGRVHA 538

Query: 543 LVKTNWLASPPLVVAYALAGNMNINLATDPLGYDRKGDPVYLKDIWPSAQEIARAV-ELV 601
            V+ N+LASPPLVVAYA+AG ++I+   DPL  D +G+PVYLKDIWP+  E+  A+ E V
Sbjct: 539 EVRMNYLASPPLVVAYAIAGRIDIDPYNDPLTTDAQGNPVYLKDIWPTQDEVNAAIAEFV 598

Query: 602 SSDMFRKEYAEVFEGTEEWKSIQVESSDTYGWQSDSTYIRLSPFFDEMQAQPAPVKDIHG 661
           +   F   YA+VF G   W+S+   ++ TY W +DSTYIR  P+F  M  + APV+DI  
Sbjct: 599 TPAEFTAAYADVFAGDARWQSLDAVATQTYDWPADSTYIRNPPYFQGMSLEVAPVEDISR 658

Query: 662 ARILAMLGDSVTTDHISPAGSIKPDSPAGRYLQNHGVERKDFNSYGSRRGNHEVMMRGTF 721
           AR LA+LGDS+TTDHISPAGSIKP+SPAG+YL  HGVE KDFNS GSRRGNHEVMMRGTF
Sbjct: 659 ARCLAVLGDSITTDHISPAGSIKPNSPAGKYLIEHGVEPKDFNSLGSRRGNHEVMMRGTF 718

Query: 722 ANIRIRNEMLPGVEGGMTRHLPGTEAMSIYDAAMLYQQEKTPLAVIAGKEYGSGSSRDWA 781
           ANIR+RN M PG EGG+T H P  E +SIYDAAM YQ E TP  VIAGKEYGSGSSRDWA
Sbjct: 719 ANIRLRNLMAPGTEGGVTLHQPSQEQLSIYDAAMRYQAEGTPAIVIAGKEYGSGSSRDWA 778

Query: 782 AKGPRLLGIRVVIAESFERIHRSNLIGMGILPLEFPQGVTRKTLGLTGEEVIDIADLQNL 841
           AKGPRLLGIR VIAES+ERIHRSNL+GMGILPL+F  G    +LGL G E  DI  L N 
Sbjct: 779 AKGPRLLGIRAVIAESYERIHRSNLVGMGILPLQFLAGENAASLGLIGTETFDIVGL-NG 837

Query: 842 RPGATIPVTLTRSDGSKETVPCRCRIDTATELTYYQNDGILHYVIRNM 889
                + V  T +DGS +T   R RIDT  E+ YY++ GIL YV+R +
Sbjct: 838 GEAKQVEVRATGADGSVKTFQARVRIDTPNEVDYYRHGGILQYVLRKL 885


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: 2129
Number of extensions: 94
Number of successful extensions: 5
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: 887
Length adjustment: 43
Effective length of query: 848
Effective length of database: 844
Effective search space:   715712
Effective search space used:   715712
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 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