Alignments for a candidate for acn in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Dinoroseobacter shibae DFL-12

Align Aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate 3608667 Dshi_2060 aconitate hydratase 2 (RefSeq)

Query= reanno::Dino:3608667
         (930 letters)



>FitnessBrowser__Dino:3608667
          Length = 930

 Score = 1824 bits (4725), Expect = 0.0
 Identities = 930/930 (100%), Positives = 930/930 (100%)

Query: 1   MSLYTAYLEEIAARKEQGLQPKPIDDAALTSEIIAQIKDPAHEHRADSLQFFIYNTLPGT 60
           MSLYTAYLEEIAARKEQGLQPKPIDDAALTSEIIAQIKDPAHEHRADSLQFFIYNTLPGT
Sbjct: 1   MSLYTAYLEEIAARKEQGLQPKPIDDAALTSEIIAQIKDPAHEHRADSLQFFIYNTLPGT 60

Query: 61  TSAAGAKAQFLKEIILGESVVAEITPDFAFELLSHMRGGPSVEVLLDIALGDDASLAAQA 120
           TSAAGAKAQFLKEIILGESVVAEITPDFAFELLSHMRGGPSVEVLLDIALGDDASLAAQA
Sbjct: 61  TSAAGAKAQFLKEIILGESVVAEITPDFAFELLSHMRGGPSVEVLLDIALGDDASLAAQA 120

Query: 121 AEVLKTQVFLYEADTDRLKAAHEAGNAVATGILQSYARAEFFTTLPEIEDEIEVVTYIAA 180
           AEVLKTQVFLYEADTDRLKAAHEAGNAVATGILQSYARAEFFTTLPEIEDEIEVVTYIAA
Sbjct: 121 AEVLKTQVFLYEADTDRLKAAHEAGNAVATGILQSYARAEFFTTLPEIEDEIEVVTYIAA 180

Query: 181 EGDISTDLLSPGNQAHSRSDRELHGKCMISEAAQKEIEALKLQHPGKRVMLIAEKGTMGV 240
           EGDISTDLLSPGNQAHSRSDRELHGKCMISEAAQKEIEALKLQHPGKRVMLIAEKGTMGV
Sbjct: 181 EGDISTDLLSPGNQAHSRSDRELHGKCMISEAAQKEIEALKLQHPGKRVMLIAEKGTMGV 240

Query: 241 GSSRMSGVNNVALWTGKQASPYVPFVNIAPVVAGTNGISPIFMTTVGVTGGIGIDLKNWV 300
           GSSRMSGVNNVALWTGKQASPYVPFVNIAPVVAGTNGISPIFMTTVGVTGGIGIDLKNWV
Sbjct: 241 GSSRMSGVNNVALWTGKQASPYVPFVNIAPVVAGTNGISPIFMTTVGVTGGIGIDLKNWV 300

Query: 301 KKVDGDGNPILNNDGNPILEQKYSVDTGTVLKIDTKARKLMSADGGEELADVSSAFSPQA 360
           KKVDGDGNPILNNDGNPILEQKYSVDTGTVLKIDTKARKLMSADGGEELADVSSAFSPQA
Sbjct: 301 KKVDGDGNPILNNDGNPILEQKYSVDTGTVLKIDTKARKLMSADGGEELADVSSAFSPQA 360

Query: 361 VEFMKAGGSYAVVFGKKLQTLAAETLGVEPTPVFAPAKEISHEGQGLTAVEKIFNANARG 420
           VEFMKAGGSYAVVFGKKLQTLAAETLGVEPTPVFAPAKEISHEGQGLTAVEKIFNANARG
Sbjct: 361 VEFMKAGGSYAVVFGKKLQTLAAETLGVEPTPVFAPAKEISHEGQGLTAVEKIFNANARG 420

Query: 421 VTPGKVLHAGSDVRVQVNIVGSQDTTGLMTSQELEAMAATVLSPTVDGAYQSGCHTASVW 480
           VTPGKVLHAGSDVRVQVNIVGSQDTTGLMTSQELEAMAATVLSPTVDGAYQSGCHTASVW
Sbjct: 421 VTPGKVLHAGSDVRVQVNIVGSQDTTGLMTSQELEAMAATVLSPTVDGAYQSGCHTASVW 480

Query: 481 DLKAQANTPRLMAFMHKFGLITARDPKGVYHSMTDVIHKVLNDITVSDWDIIIGGDSHTR 540
           DLKAQANTPRLMAFMHKFGLITARDPKGVYHSMTDVIHKVLNDITVSDWDIIIGGDSHTR
Sbjct: 481 DLKAQANTPRLMAFMHKFGLITARDPKGVYHSMTDVIHKVLNDITVSDWDIIIGGDSHTR 540

Query: 541 MSKGVAFGADSGTVALALATGEATMPIPESVKVTFKGKMADHMDFRDVVHATQAQMLAQH 600
           MSKGVAFGADSGTVALALATGEATMPIPESVKVTFKGKMADHMDFRDVVHATQAQMLAQH
Sbjct: 541 MSKGVAFGADSGTVALALATGEATMPIPESVKVTFKGKMADHMDFRDVVHATQAQMLAQH 600

Query: 601 GDNVFQGRVIEVHIGTLLADQAFTFTDWTAEMKAKASICISNDDTLIESLEIAKQRIQVM 660
           GDNVFQGRVIEVHIGTLLADQAFTFTDWTAEMKAKASICISNDDTLIESLEIAKQRIQVM
Sbjct: 601 GDNVFQGRVIEVHIGTLLADQAFTFTDWTAEMKAKASICISNDDTLIESLEIAKQRIQVM 660

Query: 661 IDKGMDNDVQMLAGLIAKANARIAEIRSGEKPALKPDDTARYFAEVVVDLDQIVEPMIAD 720
           IDKGMDNDVQMLAGLIAKANARIAEIRSGEKPALKPDDTARYFAEVVVDLDQIVEPMIAD
Sbjct: 661 IDKGMDNDVQMLAGLIAKANARIAEIRSGEKPALKPDDTARYFAEVVVDLDQIVEPMIAD 720

Query: 721 PDVHNADVSKRYTHDTIRPISYYGAEKKIDLGFVGSCMVHKGDVKIVAQMLRNLEKANGE 780
           PDVHNADVSKRYTHDTIRPISYYGAEKKIDLGFVGSCMVHKGDVKIVAQMLRNLEKANGE
Sbjct: 721 PDVHNADVSKRYTHDTIRPISYYGAEKKIDLGFVGSCMVHKGDVKIVAQMLRNLEKANGE 780

Query: 781 VKFKAPLVLAAPTYNIIDELKEEGDWDVLQKYAGFEFDDSAPKEKARTEYENILYLERPG 840
           VKFKAPLVLAAPTYNIIDELKEEGDWDVLQKYAGFEFDDSAPKEKARTEYENILYLERPG
Sbjct: 781 VKFKAPLVLAAPTYNIIDELKEEGDWDVLQKYAGFEFDDSAPKEKARTEYENILYLERPG 840

Query: 841 CNLCMGNQEKAAKGDTVLATSTRLFQGRVVADSETKKGESLLGSTPVVVLSAILGRTPTV 900
           CNLCMGNQEKAAKGDTVLATSTRLFQGRVVADSETKKGESLLGSTPVVVLSAILGRTPTV
Sbjct: 841 CNLCMGNQEKAAKGDTVLATSTRLFQGRVVADSETKKGESLLGSTPVVVLSAILGRTPTV 900

Query: 901 EEYKTAVEGINLTKFAPPLTPPIDAKSVHF 930
           EEYKTAVEGINLTKFAPPLTPPIDAKSVHF
Sbjct: 901 EEYKTAVEGINLTKFAPPLTPPIDAKSVHF 930


Lambda     K      H
   0.316    0.132    0.374 

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: 2576
Number of extensions: 84
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: 930
Length of database: 930
Length adjustment: 43
Effective length of query: 887
Effective length of database: 887
Effective search space:   786769
Effective search space used:   786769
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: 57 (26.6 bits)

This GapMind analysis is from Sep 17 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