Alignments for a candidate for acn in Stenotrophomonas chelatiphaga DSM 21508

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Stenotrophomonas chelatiphaga DSM 21508

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_057687523.1 ABB28_RS16850 aconitate hydratase AcnA

Query= SwissProt::O53166
         (943 letters)



>NCBI__GCF_001431535.1:WP_057687523.1
          Length = 917

 Score = 1103 bits (2852), Expect = 0.0
 Identities = 558/944 (59%), Positives = 694/944 (73%), Gaps = 43/944 (4%)

Query: 7   NSFGAHDTLKVGEKSYQIYRLDAVP---NTAKLPYSLKVLAENLLRNEDGS-NITKDHIE 62
           +SF     L VG K Y  + L  +    + + LPYS+K+L ENLLR+EDG   + KDHIE
Sbjct: 3   DSFSTRSQLDVGGKRYDYFSLPKLGQRFDISHLPYSMKILLENLLRHEDGGVTVGKDHIE 62

Query: 63  AIANWDPKAEPSIEIQYTPARVVMQDFTGVPCIVDLATMREAIADLGGNPDKVNPLAPAD 122
           A+A WDPKAEP IEI + PARVV+QDFTGVPC+VDLA MR+A+  LGG+P+++NP  P++
Sbjct: 63  AVATWDPKAEPEIEIAFMPARVVLQDFTGVPCVVDLAAMRDAVVKLGGSPEQINPQIPSE 122

Query: 123 LVIDHSVIADLFGRADAFERNVEIEYQRNGERYQFLRWGQGAFDDFKVVPPGTGIVHQVN 182
           LVIDHSV  D+FG+ +A + N +IE+QRN ERY FLRWGQ AFD+FKVVPP TGIVHQVN
Sbjct: 123 LVIDHSVQVDVFGKPEALDLNGKIEFQRNQERYGFLRWGQKAFDNFKVVPPNTGIVHQVN 182

Query: 183 IEYLASVVMT--RDG--VAYPDTCVGTDSHTTMVNGLGVLGWGVGGIEAEAAMLGQPVSM 238
           +E LA VVM   +DG  VAYPDT  GTDSHTTM+NG+GVLGWGVGGIEAEAAMLGQP SM
Sbjct: 183 LENLARVVMAVDKDGTQVAYPDTVFGTDSHTTMINGIGVLGWGVGGIEAEAAMLGQPSSM 242

Query: 239 LIPRVVGFRLTGEIQPGVTATDVVLTVTEMLRQHGVVGKFVEFYGEGVAEVPLANRATLG 298
           LIP+VVGF+LTG++  G TATD+VLTVT+MLR+HGVVGKFVEF+GEG+  +PLA+RAT+G
Sbjct: 243 LIPQVVGFKLTGQMPEGATATDLVLTVTQMLRKHGVVGKFVEFFGEGLQHLPLADRATIG 302

Query: 299 NMSPEFGSTAAIFPIDEETIKYLRFTGRTPEQVALVEAYAKAQGMWHDPKH-EPEFSEYL 357
           NM+PE+G+T  IFPID E++ YLR +GR  EQ+ALVEAYAKAQG+WHD      ++S  L
Sbjct: 303 NMAPEYGATCGIFPIDHESLNYLRLSGRPEEQIALVEAYAKAQGLWHDADTAHAQYSATL 362

Query: 358 ELNLSDVVPSIAGPKRPQDRIALAQAKSTFREQIYHYVGNGSPDSPHDPHSKLDEVVEET 417
           EL++  V PS+AGPKRPQDR+ L   ++ +RE +     N              +V   T
Sbjct: 363 ELDMGTVKPSLAGPKRPQDRVLLEDVQANYREALVGLTTNRDKK----------DVDVST 412

Query: 418 FPASDPGQLTFANDDVATDETVHSAAAHADGRVSNPVRVKSDELGEFVLDHGAVVIAAIT 477
           F  ++ G     N+ +A  +    A    DG+              F L  GAVVIAAIT
Sbjct: 413 F-VNEGGGTAVGNEQLAKGQ----ADVELDGKA-------------FRLKDGAVVIAAIT 454

Query: 478 SCTNTSNPEVMLGAALLARNAVEKGLTSKPWVKTTIAPGSQVVNDYYDRSGLWPYLEKLG 537
           SCTNTSNP VM+GA LLARNA  +GL  +PWVKT++ PGS+VV DY  ++G+   LEKLG
Sbjct: 455 SCTNTSNPAVMIGAGLLARNAAARGLNRQPWVKTSLGPGSRVVTDYLSKAGVLTELEKLG 514

Query: 538 FYLVGYGCTTCIGNSGPLPEEISKAVNDNDLSVTAVLSGNRNFEGRINPDVKMNYLASPP 597
           FY+VGYGCTTCIGNSGPLP E+S  +   DL VT+VLSGNRNFEGR++P+VKMNYLASPP
Sbjct: 515 FYVVGYGCTTCIGNSGPLPAEVSAGIALGDLVVTSVLSGNRNFEGRVHPEVKMNYLASPP 574

Query: 598 LVIAYALAGTMDFDFQTQPLGQDKDGKNVFLRDIWPSQQDVSDTIAAAINQEMFTRNYAD 657
           LV+AYA+AGT D D  T+PLG   DG+ V+LRDIWPS +++ D IAA +  EMF +NYAD
Sbjct: 575 LVVAYAIAGTTDIDLTTEPLGTGSDGQPVYLRDIWPSNKEIGDVIAATLGPEMFKQNYAD 634

Query: 658 VFKGDDRWRNLPTPSGNTFEWDPNSTYVRKPPYFEGMTAKPEPVGNISGARVLALLGDSV 717
           VFKGD RW  + +P G+ +EWD  STY++ PPYF+GMT +   + ++ GARV+ L GDS+
Sbjct: 635 VFKGDSRWNTIASPDGDLYEWDDGSTYIKNPPYFDGMTMQVGSIDDVHGARVMGLFGDSI 694

Query: 718 TTDHISPAGAIKPGTPAARYLDEHGVDRKDYNSFGSRRGNHEVMIRGTFANIRLRNQLLD 777
           TTDHISPAG IK  +PA R+L E GV   D+NS+GSRRGN +VM+RGTFANIR++N +  
Sbjct: 695 TTDHISPAGNIKKESPAGRFLQERGVQPADFNSYGSRRGNDDVMVRGTFANIRIKNLMFG 754

Query: 778 DVSGGYTRDFTQPGG--PQAFIYDAAQNYAAQHIPLVVFGGKEYGSGSSRDWAAKGTLLL 835
              GG T  +   GG   +  IYDAA  Y A  +PLVV  GKEYG+GSSRDWAAKGTLLL
Sbjct: 755 GEEGGNTLYYPASGGEPEKLAIYDAAIKYKADGVPLVVLAGKEYGTGSSRDWAAKGTLLL 814

Query: 836 GVRAVIAESFERIHRSNLIGMGVIPLQFPEGKSASSLGLDGTEVFDITGIDVLNDGKTPK 895
           GV+AVIAESFERIHRSNL+GMGV+PLQF  G++A SLGLDG+EVFDITG   L DG + K
Sbjct: 815 GVKAVIAESFERIHRSNLVGMGVLPLQFRNGENAQSLGLDGSEVFDITG---LKDGAS-K 870

Query: 896 TVCVQATKGDGATIEFDAVVRIDTPGEADYYRNGGILQYVLRNI 939
              V A K DG  + F+A V + TP E +Y+R+GG+LQYVLR +
Sbjct: 871 RATVAAKKADGTVVTFEASVMLLTPKEVEYFRHGGLLQYVLRQL 914


Lambda     K      H
   0.316    0.136    0.403 

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: 2508
Number of extensions: 133
Number of successful extensions: 8
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: 943
Length of database: 917
Length adjustment: 43
Effective length of query: 900
Effective length of database: 874
Effective search space:   786600
Effective search space used:   786600
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 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