Alignments for a candidate for acn in Pedobacter sp. GW460-11-11-14-LB5

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Pedobacter sp. GW460-11-11-14-LB5

Align Aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate CA265_RS16400 CA265_RS16400 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase

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



>FitnessBrowser__Pedo557:CA265_RS16400
          Length = 921

 Score = 1420 bits (3676), Expect = 0.0
 Identities = 709/918 (77%), Positives = 807/918 (87%), Gaps = 3/918 (0%)

Query: 1   MSLYTAYLEEIAARKEQGLQPKPIDDAALTSEIIAQIKDPAHEHRADSLQFFIYNTLPGT 60
           MS+Y  Y++EI  RK QGL PKPID A L SEII QIK+  + +R +++ FFIYNTLPGT
Sbjct: 1   MSIYNDYIQEIEDRKAQGLHPKPIDGAELLSEIITQIKNVNNINREEAVNFFIYNTLPGT 60

Query: 61  TSAAGAKAQFLKEIILGESVVAEITPDFAFELLSHMRGGPSVEVLLDIALGDDASLAAQA 120
           T+AA  KAQFLKEIIL E +VAEITPDFAFELLSHM+GGPS++VLLDIAL D+   A +A
Sbjct: 61  TAAAAVKAQFLKEIILAEVIVAEITPDFAFELLSHMKGGPSIKVLLDIALADNGDKAKKA 120

Query: 121 AEVLKTQVFLYEADTDRLKAAHEAGNAVATGILQSYARAEFFTTLPEIEDEIEVVTYIAA 180
           A+VLKTQV+LY+ADTDRLK A+  GN +A  IL+SYA+AEFFT LPE+ +EI+VVT+IA 
Sbjct: 121 ADVLKTQVYLYDADTDRLKDAYNNGNEIAKEILESYAKAEFFTKLPEVAEEIKVVTFIAG 180

Query: 181 EGDISTDLLSPGNQAHSRSDRELHGKCMISEAAQKEIEALKLQHPGKRVMLIAEKGTMGV 240
            GDISTDLLSPGNQAHSRSDRELHGKCMI+  AQ+EI+AL+ QHP K VML+AEKGTMGV
Sbjct: 181 IGDISTDLLSPGNQAHSRSDRELHGKCMITPEAQEEIKALQAQHPDKSVMLVAEKGTMGV 240

Query: 241 GSSRMSGVNNVALWTGKQASPYVPFVNIAPVVAGTNGISPIFMTTVGVTGGIGIDLKNWV 300
           GSSRMSGVNNVALWTGK++SPYVPFVNIAP+V GTNGISPIF+TTV VTGGIGIDL+NWV
Sbjct: 241 GSSRMSGVNNVALWTGKRSSPYVPFVNIAPIVGGTNGISPIFLTTVDVTGGIGIDLQNWV 300

Query: 301 KKVDGDGNPILNNDGNPILEQKYSVDTGTVLKIDTKARKLMSADGGEELADVSSAFSPQA 360
           KK D +GN I N    PILEQ++SV+TGTVL I+TK +KL +  G +EL D+S A +PQ 
Sbjct: 301 KKTDENGNVIRNEKDEPILEQRFSVETGTVLTINTKTKKLYN--GEQELIDISKALTPQK 358

Query: 361 VEFMKAGGSYAVVFGKKLQTLAAETLGVEPTPVFAPAKEISHEGQGLTAVEKIFNANARG 420
           +EFMKAGGSYA++FGKK+QT AA+TLG+E + VFAPAKE+S+EGQGLTAVEKIFN NA G
Sbjct: 359 MEFMKAGGSYAIIFGKKIQTFAAKTLGIEASSVFAPAKEVSYEGQGLTAVEKIFNRNAVG 418

Query: 421 VTPGKVLHAGSDVRVQVNIVGSQDTTGLMTSQELEAMAATVLSPTVDGAYQSGCHTASVW 480
           +T GKVLHAGSDVRV+VNIVGSQDTTGLMT+QELEAMAATV+SP VDGAYQSGCHTASVW
Sbjct: 419 LTQGKVLHAGSDVRVEVNIVGSQDTTGLMTAQELEAMAATVISPIVDGAYQSGCHTASVW 478

Query: 481 DLKAQANTPRLMAFMHKFGLITARDPKGVYHSMTDVIHKVLNDITVSDWDIIIGGDSHTR 540
           D KAQAN P+LM FM+ FG+ITARDPKG YHSMTDVIHKVLNDIT+ +W IIIGGDSHTR
Sbjct: 479 DKKAQANIPKLMKFMNDFGVITARDPKGEYHSMTDVIHKVLNDITIDEWAIIIGGDSHTR 538

Query: 541 MSKGVAFGADSGTVALALATGEATMPIPESVKVTFKGKMADHMDFRDVVHATQAQMLAQH 600
           MSKGVAFGADSGTVALALATGEA+MPIPESVKVTFKG M +HMDFRDVVHATQ QML Q 
Sbjct: 539 MSKGVAFGADSGTVALALATGEASMPIPESVKVTFKGLMKEHMDFRDVVHATQLQMLQQF 598

Query: 601 -GDNVFQGRVIEVHIGTLLADQAFTFTDWTAEMKAKASICISNDDTLIESLEIAKQRIQV 659
            G+NVFQGR+IEVHIGTLLADQAFTFTDWTAEMKAKASICIS DDTLI+SLEIAK RIQ+
Sbjct: 599 DGENVFQGRIIEVHIGTLLADQAFTFTDWTAEMKAKASICISQDDTLIQSLEIAKNRIQI 658

Query: 660 MIDKGMDNDVQMLAGLIAKANARIAEIRSGEKPALKPDDTARYFAEVVVDLDQIVEPMIA 719
           MIDKGMDN  Q+L GLI KAN RI EI++G KPAL PDD A+Y+AEVV+DLD I EPMIA
Sbjct: 659 MIDKGMDNHNQVLQGLINKANKRIEEIKTGIKPALMPDDNAKYYAEVVIDLDLIEEPMIA 718

Query: 720 DPDVHNADVSKRYTHDTIRPISYYGAEKKIDLGFVGSCMVHKGDVKIVAQMLRNLEKANG 779
           DPDV+NADVSKRYTHDTIR +++YG +KK+DLGFVGSCMVHK D+KIV+QML+N+E   G
Sbjct: 719 DPDVNNADVSKRYTHDTIRDLTFYGGDKKVDLGFVGSCMVHKDDLKIVSQMLKNVETQTG 778

Query: 780 EVKFKAPLVLAAPTYNIIDELKEEGDWDVLQKYAGFEFDDSAPKEKARTEYENILYLERP 839
           +V+FKAPLV+AAPTYNIIDELK EGDW+ LQKY+GFEF D+ PK  ARTEYENI+YLERP
Sbjct: 779 KVEFKAPLVVAAPTYNIIDELKAEGDWEYLQKYSGFEFSDALPKSAARTEYENIMYLERP 838

Query: 840 GCNLCMGNQEKAAKGDTVLATSTRLFQGRVVADSETKKGESLLGSTPVVVLSAILGRTPT 899
           GCNLCMGNQEKAAKGDTV+ATSTRLFQGRVV D + KKGESLL STPVVVLSAILGR P+
Sbjct: 839 GCNLCMGNQEKAAKGDTVMATSTRLFQGRVVEDKDGKKGESLLASTPVVVLSAILGRIPS 898

Query: 900 VEEYKTAVEGINLTKFAP 917
           +EEYK AVEGINLTKF P
Sbjct: 899 IEEYKVAVEGINLTKFTP 916


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: 2223
Number of extensions: 83
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: 930
Length of database: 921
Length adjustment: 43
Effective length of query: 887
Effective length of database: 878
Effective search space:   778786
Effective search space used:   778786
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