Alignments for a candidate for acn in Herbaspirillum aquaticum IEH 4430

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Herbaspirillum aquaticum IEH 4430

Align Aconitate hydratase A; ACN; Aconitase; (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; RNA-binding protein; EC 4.2.1.3; EC 4.2.1.99 (characterized)
to candidate WP_088753350.1 CEJ45_RS00705 aconitate hydratase AcnA

Query= SwissProt::P70920
         (906 letters)



>NCBI__GCF_002213425.1:WP_088753350.1
          Length = 903

 Score =  963 bits (2490), Expect = 0.0
 Identities = 507/901 (56%), Positives = 639/901 (70%), Gaps = 24/901 (2%)

Query: 16  GAKTYVYYSLPTAEKNGLKGISKLPYSMKVLLENLLRNEDGRSVKKADIVAVSKWLRKKS 75
           G+K   +YSLP  +K+    IS+LP S++++LE++LRN DG+ V +  +  ++ W  K +
Sbjct: 16  GSKKGKFYSLPALQKSLGVNISRLPVSIRIVLESVLRNCDGQKVTEEHVKQLANWGAKAA 75

Query: 76  LEHEIAFRPARVLMQDFTGVPAVVDLAAMRNAMQKLGGDAEKINPLVPVDLVIDHSVIVN 135
              EI F  ARV++QDFTGVP + DLAAMRN   KLG + + I PLVPVDLV+DHSV ++
Sbjct: 76  RVDEIPFVVARVVLQDFTGVPLLADLAAMRNVASKLGKNPKNIEPLVPVDLVVDHSVQID 135

Query: 136 FFGDNKAFAKNVTEEYKQNQERYEFLKWGQAAFSNFSVVPPGTGICHQVNLEYLSQTVWT 195
            F + KA   N+  E+ +N ERY+F+KWG  AF  F VVPPG GI HQVNLEYL++ V  
Sbjct: 136 HFREKKALDLNMKLEFSRNNERYQFMKWGMQAFDTFGVVPPGFGIVHQVNLEYLARGVHN 195

Query: 196 KKEKMTVGKKTGTFEVAYPDSLVGTDSHTTMVNGLAVLGWGVGGIEAEACMLGQPLSMLL 255
           K         TG +   YPD+LVGTDSHTTM+NG+ V+GWGVGGIEAEA MLGQP+  L 
Sbjct: 196 K---------TGVY---YPDTLVGTDSHTTMINGIGVVGWGVGGIEAEAGMLGQPVYFLT 243

Query: 256 PNVVGFKLKGAMKEGVTATDLVLTVTQMLRKLGVVGKFVEFFGPGLDHLSVADKATIANM 315
           P+VVG  L GA++EGVTATDLVLT+T++LR+  VVGKFVEFFG G + LS+ D+ATIANM
Sbjct: 244 PDVVGVNLTGALREGVTATDLVLTITELLRQTKVVGKFVEFFGEGTESLSLTDRATIANM 303

Query: 316 APEYGATCGFFPVDAAAIDYLKTSGRAAPRVALVQAYAKAQGLFRTAKSADPVFTETLTL 375
           APEYGAT GFFPVD A IDY K +GR    +   +AY KAQGL+   K+    +T+ ++L
Sbjct: 304 APEYGATMGFFPVDDATIDYFKGTGRTKAEIDAFEAYFKAQGLYGVPKAGQIDYTQEVSL 363

Query: 376 DLADVVPSMAGPKRPEGRIALPSVAEGFS-----VALANEYKKTEEPAKRFAVEGKKYEI 430
           DL  V PS+AGPKRP+ RI + +V   FS         N + K  E            ++
Sbjct: 364 DLGTVAPSLAGPKRPQDRIEIGNVKSTFSDLFTKPTAENGFNKKAEDLTASYKNADGVDV 423

Query: 431 GHGDVVIAAITSCTNTSNPSVLIGAGLLARNAAAKGLKAKPWVKTSLAPGSQVVAAYLAD 490
            +GDV+IAAITSCTNTSNPSVL+ AGLLA+ A   GLK  P +KTSLAPGS+VV  YL  
Sbjct: 424 HNGDVLIAAITSCTNTSNPSVLLAAGLLAKKAVEAGLKVAPHIKTSLAPGSRVVTKYLEA 483

Query: 491 SGLQAHLDKVGFNLVGFGCTTCIGNSGPLPEEISKSINDNGIVAAAVLSGNRNFEGRVSP 550
           +GL  +L+K+GF +  +GCTTCIGN+G L   ++++I  N +VAAAVLSGNRNFE R+ P
Sbjct: 484 AGLLPYLEKLGFGVTAYGCTTCIGNAGDLTPAMNEAIVKNDVVAAAVLSGNRNFEARIHP 543

Query: 551 DVQANYLASPPLVVAHALAGSVTKNLAVEPLGEGKDGKPVYLKDIWPTSKEINAFMKKFV 610
           +++AN+LASPPLVVA+A+AG+VT++L  EP+G+GK GK VYL DIWPTS+EI   +K  +
Sbjct: 544 NIRANFLASPPLVVAYAIAGNVTRDLMTEPVGKGKGGKNVYLGDIWPTSQEIEKLLKFAM 603

Query: 611 TASIFKKKYADVFKGDTN--WRKIKTV-ESETYRWNMSSTYVQNPPYFEGMKKEPE-PVT 666
            A  FK+ YADV KG     W  IK V + E Y W  SSTY+  PP+FE   +EP+   T
Sbjct: 604 NAKTFKENYADV-KGAPGKLWEAIKGVAKGEVYNW-PSSTYIAEPPFFENFSEEPKAAAT 661

Query: 667 DIVEARILAMFGDKITTDHISPAGSIKLTSPAGKYLSEHQVRPADFNQYGTRRGNHEVMM 726
            I  AR L +FGD ITTDHISPAGSIK +SPAGK+L  + V  ADFN YG+RRGNHE+MM
Sbjct: 662 GISGARALGVFGDSITTDHISPAGSIKESSPAGKWLQANGVLKADFNSYGSRRGNHEIMM 721

Query: 727 RGTFANIRIKNFMLKG-ADGNIPEGGLTKHWPDGEQMSIYDAAMKYQQEQVPLVVFAGAE 785
           RGTFAN+RIKN M+    DG+  EGG+T H P GE+MSIYDAAMKY  E  P +VF G E
Sbjct: 722 RGTFANVRIKNLMIPAKEDGSRVEGGITIHQPSGEEMSIYDAAMKYVAEGTPTMVFGGEE 781

Query: 786 YGNGSSRDWAAKGTRLLGVRAVICQSFERIHRSNLVGMGVLPLTFEEGTSWSSLGLKGDE 845
           YG GSSRDWAAKGT+LLGV+AVI +SFERIHRSNLVGMGVLPL F    S  SLG+ G+E
Sbjct: 782 YGTGSSRDWAAKGTQLLGVKAVIARSFERIHRSNLVGMGVLPLQFLGNDSVQSLGITGEE 841

Query: 846 KVTLRGLVGDLKPRQKLTAEIVSGDGSLQRVSLLCRIDTLDELDYYRNGGILHYVLRKLA 905
              L+GL G++KP+Q+ T  I   +G  Q V LL RIDT  E+DYY++GGIL +VLR+L 
Sbjct: 842 SFDLKGLEGEIKPQQEATLVIHRKNGQTQEVKLLLRIDTPIEVDYYKHGGILPFVLRQLL 901

Query: 906 A 906
           A
Sbjct: 902 A 902


Lambda     K      H
   0.317    0.134    0.393 

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: 2159
Number of extensions: 99
Number of successful extensions: 6
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: 906
Length of database: 903
Length adjustment: 43
Effective length of query: 863
Effective length of database: 860
Effective search space:   742180
Effective search space used:   742180
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