Alignments for a candidate for acn in Pseudomonas litoralis 2SM5

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Pseudomonas litoralis 2SM5

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_090272412.1 BLU11_RS05430 aconitate hydratase AcnA

Query= SwissProt::Q8ZP52
         (891 letters)



>NCBI__GCF_900105005.1:WP_090272412.1
          Length = 911

 Score = 1229 bits (3181), Expect = 0.0
 Identities = 615/908 (67%), Positives = 719/908 (79%), Gaps = 19/908 (2%)

Query: 1   MSSTLREASKDTLQAKDKTYHYYSLPLAAKSLGDIARLPKSLKVLLENLLRWQDGESVTD 60
           MSS     +  +LQ   +TY Y+SLP A + LG+I RLP SLKVLLENLLR +DG++VT 
Sbjct: 1   MSSINSLQTLSSLQVGGRTYQYHSLPKAGELLGEINRLPVSLKVLLENLLRHEDGDTVTR 60

Query: 61  EDIQALAGWLKNAHADREIAWRPARVLMQDFTGVPAVVDLAAMREAVKRLGGDTSKVNPL 120
           EDIQA+A W+ N H+DREI +RPARVLMQDFTGVPAVVDLAAMR+AV R GGD  ++NPL
Sbjct: 61  EDIQAMADWMINRHSDREIQYRPARVLMQDFTGVPAVVDLAAMRDAVARAGGDPQRINPL 120

Query: 121 SPVDLVIDHSVTVDHFGDDDAFEENVRLEMERNHERYMFLKWGKQAFSRFSVVPPGTGIC 180
           SPVDLVIDHSV VDHFGD  AF+ NV +E++RN ERY FL+WG++AF+ F VVPPGTGIC
Sbjct: 121 SPVDLVIDHSVMVDHFGDAAAFQGNVAMEIQRNGERYAFLRWGQKAFNNFRVVPPGTGIC 180

Query: 181 HQVNLEYLGKAVWSELQDGEWIAYPDSLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQ 240
           HQVNLEYL ++VW+   DG+  AYPD+LVGTDSHTTM+NGLGVLGWGVGGIEAEAAMLGQ
Sbjct: 181 HQVNLEYLAQSVWAAEVDGQSWAYPDTLVGTDSHTTMVNGLGVLGWGVGGIEAEAAMLGQ 240

Query: 241 PVSMLIPDVVGFKLTGKLREGITATDLVLTVTQMLRKHGVVGKFVEFYGDGLDSLPLADR 300
           PVSMLIP+VVGFKLTGKLREG+TATDLVLTVTQMLRKHGVVGKFVEFYGDGL  LPLADR
Sbjct: 241 PVSMLIPEVVGFKLTGKLREGMTATDLVLTVTQMLRKHGVVGKFVEFYGDGLADLPLADR 300

Query: 301 ATIANMSPEYGATCGFFPIDAITLEYMRLSGRSDDLVELVETYAKAQGMWRNPGDEPVFT 360
           ATIANM+PEYGATCGFFPID ITL Y+RL+GR  ++VE VE Y+KAQGMWR PG EPVFT
Sbjct: 301 ATIANMAPEYGATCGFFPIDEITLGYLRLTGRPAEVVERVEAYSKAQGMWREPGHEPVFT 360

Query: 361 STLELDMGDVEASLAGPKRPQDRVALGDVPKAFAASAELELNTAQRDRQPVD-------- 412
            TL LDM +VE SLAGP+RPQDRV L DVPKAF     L+  +A RD + ++        
Sbjct: 361 DTLHLDMNEVEPSLAGPRRPQDRVRLSDVPKAFDELLALQ-TSAVRDVERLEDEGGGGTA 419

Query: 413 ---------YTMNGQPYQLPDGAVVIAAITSCTNTSNPSVLMAAGLLAKKAVTLGLKRQP 463
                     T++G+ + L +GAVVIAAITSCTNTSNPSV+MAAGLLA+KA+  G++R+P
Sbjct: 420 VGGPSAEVCVTIDGEEHVLKNGAVVIAAITSCTNTSNPSVMMAAGLLARKAIERGIQRKP 479

Query: 464 WVKASLAPGSKVVSDYLAQAKLTPYLDELGFNLVGYGCTTCIGNSGPLPEPIETAIKKGD 523
           WVK+SLAPGSKVV+DYL +A LTPYLD+LGFNLVGYGCTTCIGNSGPLPEPI  AI + D
Sbjct: 480 WVKSSLAPGSKVVTDYLERAGLTPYLDQLGFNLVGYGCTTCIGNSGPLPEPISHAISEHD 539

Query: 524 LTVGAVLSGNRNFEGRIHPLVKTNWLASPPLVVAYALAGNMNINLATDPLGYDRKGDPVY 583
           L V AVLSGNRNFEGR+H  VK NWLASPPLVVAYALAG+  ++L  +PLG DR   PVY
Sbjct: 540 LVVSAVLSGNRNFEGRVHQQVKANWLASPPLVVAYALAGDSRLDLQEEPLGLDRDNKPVY 599

Query: 584 LKDIWPSAQEIARAVELVSSDMFRKEYAEVFEGTEEWKSIQVESSDTYGWQSDSTYIRLS 643
           L+D+WPS  EIA AV LV   MFR  YA+VF G E W+SI V   DTY W   STY++  
Sbjct: 600 LRDLWPSNAEIAEAVALVEDSMFRSRYADVFTGDEHWQSIAVSGGDTYNWDGQSTYVQNP 659

Query: 644 PFFDEMQAQPAPVKDIHGARILAMLGDSVTTDHISPAGSIKPDSPAGRYLQNHGVERKDF 703
           P+F+ +     P++ IH AR+LA+ GDS+TTDHISPAG+IK  SPAG YLQ  GV+ +DF
Sbjct: 660 PYFERIDQPIEPLQPIHQARVLAVFGDSITTDHISPAGNIKSSSPAGEYLQRLGVKPEDF 719

Query: 704 NSYGSRRGNHEVMMRGTFANIRIRNEMLPGVEGGMTRHLPGTEAMSIYDAAMLYQQEKTP 763
           NSYGSRRGNHEVMMRGTFANIRIRN ML G EGG+T H P +E MSIYDAAM YQQE TP
Sbjct: 720 NSYGSRRGNHEVMMRGTFANIRIRNRMLGGEEGGLTIHTPSSERMSIYDAAMRYQQEGTP 779

Query: 764 LAVIAGKEYGSGSSRDWAAKGPRLLGIRVVIAESFERIHRSNLIGMGILPLEFPQGVTRK 823
           L V+AGKEYG+GSSRDWAAKG  LLG++ VIAESFERIHRSNL+GMG+LPL+F  G    
Sbjct: 780 LVVLAGKEYGTGSSRDWAAKGTNLLGVKAVIAESFERIHRSNLVGMGVLPLQFVNGQNAP 839

Query: 824 TLGLTGEEVIDIADL-QNLRPGATIPVTLTRSDGSKETVPCRCRIDTATELTYYQNDGIL 882
           TL L G EV+DI  +  NLRPG  + +  TRS+G +      CRIDT+ E+ Y++  GIL
Sbjct: 840 TLQLDGHEVLDIPGIDDNLRPGQILKIKATRSNGQQIEFEVVCRIDTSNEVDYFKAGGIL 899

Query: 883 HYVIRNML 890
           HYV+R +L
Sbjct: 900 HYVLRELL 907


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: 2239
Number of extensions: 94
Number of successful extensions: 4
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: 911
Length adjustment: 43
Effective length of query: 848
Effective length of database: 868
Effective search space:   736064
Effective search space used:   736064
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 2024 update 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