Alignments for a candidate for acn in Brevibacterium jeotgali SJ5-8

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Brevibacterium jeotgali SJ5-8

Align Aconitate hydratase A; ACN; Aconitase; (2R,3S)-2-methylisocitrate dehydratase; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate dehydratase; IP210; Iron-responsive protein-like; IRP-like; Major iron-containing protein; MICP; Probable 2-methyl-cis-aconitate hydratase; RNA-binding protein; EC 4.2.1.3; EC 4.2.1.99 (characterized)
to candidate WP_101589524.1 BJEO58_RS11005 aconitate hydratase AcnA

Query= SwissProt::P37032
         (891 letters)



>NCBI__GCF_900169175.1:WP_101589524.1
          Length = 894

 Score = 1043 bits (2696), Expect = 0.0
 Identities = 519/896 (57%), Positives = 662/896 (73%), Gaps = 17/896 (1%)

Query: 6   DSLSTKSQLTVDGKTYNYYSLKEAENKHFKGINRLPYSLKVLLENLLRFEDGNTVTTKDI 65
           DS ++KS L V+GK Y  + L   E     G  +LP+SLKVLLENLLR EDG  +T   I
Sbjct: 5   DSFTSKSMLEVNGKNYEIFRLDAVE-----GSQKLPFSLKVLLENLLRTEDGANITADHI 59

Query: 66  KAIADWLHNKTSQHEIAFRPTRVLMQDFTGVPAVVDLAAMRTAIVKMGGNADKISPLSPV 125
           + +A W       HEI F P RV+MQDFTGVP +VDLA MR A+ ++GG+ADK++PL+P 
Sbjct: 60  RTLASWDPTADPSHEIQFTPARVVMQDFTGVPCIVDLATMREAVKELGGDADKVNPLAPA 119

Query: 126 DLVIDHSVMVDKFASADALEVNTKIEIERNKERYEFLRWGQKAFSNFQVVPPGTGICHQV 185
           +LVIDHSV +D F + +A+E N  IE +RN ERY+FLRWGQ AF +F+VVPPG GI HQV
Sbjct: 120 ELVIDHSVQIDSFGNTNAIERNMDIEYQRNGERYQFLRWGQTAFDDFKVVPPGMGIVHQV 179

Query: 186 NLEYLGKTVWNSENDGQLYAYPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQPVS 245
           N+EYL + +   E DG L AYPDTLVGTDSHTTM+NGLGVLGWGVGGIEAEAAMLGQPVS
Sbjct: 180 NIEYLARVIMPREVDGVLRAYPDTLVGTDSHTTMVNGLGVLGWGVGGIEAEAAMLGQPVS 239

Query: 246 MLIPEVIGFKLSGKLKEGITATDLVLTVTQMLRKKGVVGKFVEFYGPGLNDLPLADRATI 305
           MLIP V+GFKL+G +  G+TATD+VLT+T MLR+ GVVGKFVEFYG G++ +PLA+RATI
Sbjct: 240 MLIPPVVGFKLTGGIPSGVTATDVVLTITDMLRQHGVVGKFVEFYGKGVSAVPLANRATI 299

Query: 306 SNMAPEYGATCGFFPVDKETIKYLELTGRDKHTIALVEAYAKAQGMWYDKDNEEPVFTDS 365
            NM+PE+G+T   FP+D+ T+ YL LTGRD+  +ALVE YAK QG+W+D +  E  F++ 
Sbjct: 300 GNMSPEFGSTAAMFPIDEVTLDYLRLTGRDEDQMALVETYAKEQGLWHDPE-AEIEFSEY 358

Query: 366 LHLDLGSVEPSLAGPKRPQDKVNLSSLPVEF----NNFLIEVGKEKEKEKTFAVKNKDFQ 421
           L LDL +V PS++GPKRPQD++ LS    +F    +N+  + G E++         ++F+
Sbjct: 359 LELDLSTVVPSISGPKRPQDRIELSDAKSQFAKDIHNY-AQPGDEQKSAPVATADGREFE 417

Query: 422 MKHGHVVIAAITSCTNTSNPSVLMAAGLVAKKAIEKGLQRKPWVKSSLAPGSKVVTDYLR 481
           + +G V IA+ITSCTNTSNPSV+MAAGLVA+KA EKGL  KPWVK+S+APGSKVVT+Y  
Sbjct: 418 LTNGAVAIASITSCTNTSNPSVMMAAGLVARKAREKGLSSKPWVKTSIAPGSKVVTEYYE 477

Query: 482 HAGLQTYLDQLGFNLVGYGCTTCIGNSGPLPDDISHCVAEHDLVVSSVLSGNRNFEGRVH 541
            AGL   L+ L F +VGYGCTTCIGNSGPL ++IS  + ++DL VS+VLSGNRNFEGR+ 
Sbjct: 478 KAGLIPDLEALNFYIVGYGCTTCIGNSGPLEEEISQSIQDNDLSVSAVLSGNRNFEGRIS 537

Query: 542 PQVRANWLASPPLVVAYALCGTTCSDLSREPIGQDKEGNDVYLKDIWPSNEEIAAEV-AK 600
           P V+ N+LASPPLV+AYAL GT   D   +P+GQD +GNDVYLKDIWP+ EEI   + + 
Sbjct: 538 PDVKMNYLASPPLVIAYALAGTMDFDFEGQPLGQDTDGNDVYLKDIWPAPEEIEELIQSS 597

Query: 601 VSGTMFRKEYAEVFKGDAHWQAIQTSSGQTYEWNPDSTYIQHPPFFENLSLKPEPLKPIK 660
           +S  MF  EY  +F GD  W+ + T SG  +EW   STY++ PP+F+ ++L+  P++ +K
Sbjct: 598 ISTDMFTSEYGTIFDGDHRWKELDTPSGNVFEWEDSSTYVRKPPYFDGMTLETTPVEDVK 657

Query: 661 QAYVLALFGDSITTDHISPAGSIKASSPAGLYLKSKGVDEKDFNSYGSRRGNHEVMMRGT 720
            A VLA  GDS+TTDHISPAGS KA +PAG YL   GV+ KDFNSYGSRRGNHEVM+RGT
Sbjct: 658 GARVLAKLGDSVTTDHISPAGSFKADTPAGRYLVENGVERKDFNSYGSRRGNHEVMIRGT 717

Query: 721 FANIRIRNEMTPGQEGGVTR-YVPTGETM-SIYDAAMRYQENQQDLVIIAGKEYGTGSSR 778
           FANIR++N++  G +GG TR +   G    +IYDA+  YQ     LV++ GKEYG+GSSR
Sbjct: 718 FANIRLQNQLLDGVQGGFTRDFTQEGAPQTTIYDASQNYQAAGIPLVVLGGKEYGSGSSR 777

Query: 779 DWAAKGTNLLGVKAVITESFERIHRSNLIGMGILPLQFKEGTTRKTLKLDGSERISIEIS 838
           DWAAKGT LLGV AVITESFERIHRSNLIGMG+LP+QF  G + ++L LDG+E   I   
Sbjct: 778 DWAAKGTKLLGVSAVITESFERIHRSNLIGMGVLPMQFPAGESAESLGLDGTETFDISGV 837

Query: 839 DKLTPG---AMVPVTIERQDGDIEKIETLCRIDTADELEYYKNGGILQYVLRKISS 891
            KL  G   + + VT  + DG   + + + RIDT  E +YY+NGGILQYVLR++++
Sbjct: 838 TKLNEGTTPSTLHVTATKDDGSTVEFDAVLRIDTPGEADYYRNGGILQYVLRQLAT 893


Lambda     K      H
   0.316    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: 2066
Number of extensions: 100
Number of successful extensions: 7
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: 894
Length adjustment: 43
Effective length of query: 848
Effective length of database: 851
Effective search space:   721648
Effective search space used:   721648
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