Alignments for a candidate for acn in Pseudoalteromonas arctica A 37-1-2

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Pseudoalteromonas arctica A 37-1-2

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_010554785.1 PARC_RS00780 aconitate hydratase AcnA

Query= SwissProt::O53166
         (943 letters)



>NCBI__GCF_000238395.3:WP_010554785.1
          Length = 914

 Score = 1067 bits (2759), Expect = 0.0
 Identities = 542/939 (57%), Positives = 681/939 (72%), Gaps = 33/939 (3%)

Query: 7   NSFGAHDTLKVGEKSYQIYRLDAVPNTAK-LPYSLKVLAENLLRNEDGSNITKDHIEAIA 65
           NSF     L +  + Y I+ L  + + AK LP+SLKVL ENLLRNEDG+NI +  I+A+ 
Sbjct: 3   NSFDTQHQLTINGEQYHIHSLKGLGDKAKRLPFSLKVLLENLLRNEDGANIKEQDIQALL 62

Query: 66  NWDPKAEPSIEIQYTPARVVMQDFTGVPCIVDLATMREAIADLGGNPDKVNPLAPADLVI 125
           NWDP+A+P+ E+ +TPARVVMQDFTGVP IVDLA MR+A+  LGG+P K+NPL+PA+LVI
Sbjct: 63  NWDPQAKPASEVAFTPARVVMQDFTGVPAIVDLAAMRDAMEKLGGDPAKINPLSPAELVI 122

Query: 126 DHSVIADLFGRADAFERNVEIEYQRNGERYQFLRWGQGAFDDFKVVPPGTGIVHQVNIEY 185
           DHSV  D +G   AF+ N ++EY RN ERY+FLRWGQ AFD+ KVVPP TGIVHQVN+EY
Sbjct: 123 DHSVQVDGYGNDGAFDLNAKLEYDRNKERYEFLRWGQTAFDNLKVVPPATGIVHQVNLEY 182

Query: 186 LASVVMT--RDG--VAYPDTCVGTDSHTTMVNGLGVLGWGVGGIEAEAAMLGQPVSMLIP 241
           LA VV    RDG   AYPDT VGTDSHTTM+NGLGVLGWGVGGIEAEAAMLGQP+S+LIP
Sbjct: 183 LARVVFNEERDGKKFAYPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQPISLLIP 242

Query: 242 RVVGFRLTGEIQPGVTATDVVLTVTEMLRQHGVVGKFVEFYGEGVAEVPLANRATLGNMS 301
           +VVG +L+G +  G TATD+VLTVTE+LR HGVVGKFVEFYG+G+A++PLA+RAT+ NM+
Sbjct: 243 QVVGMKLSGRLPEGTTATDLVLTVTEILRNHGVVGKFVEFYGDGLADLPLADRATIANMA 302

Query: 302 PEFGSTAAIFPIDEETIKYLRFTGRTPEQVALVEAYAKAQGMWHDPKHEPEFSEYLELNL 361
           PE+G+T  IFPID+ETI YLR T R    + ++E YAK QG+W +   E  +++ LEL L
Sbjct: 303 PEYGATCGIFPIDDETINYLRLTNRDESHLKVIEDYAKHQGLWRNDGDEASYTDTLELKL 362

Query: 362 SDVVPSIAGPKRPQDRIALAQAKSTFREQIYHYVGNGSPDSPHDPHSKLDEVVEETFPAS 421
            DVVPS+AGPKRPQDRI+L +A     + + ++          +  ++ D   EE     
Sbjct: 363 GDVVPSLAGPKRPQDRISLDKAGEVISQHLKNF--------QDERMARRDNSDEEQARIE 414

Query: 422 DPGQLTFANDDVATDETVHSAAAHADGRVSNPVRVKSDELGEFVLDHGAVVIAAITSCTN 481
             G  T  N D   +E     AA         V+ K  E   F L+ GA VIAAITSCTN
Sbjct: 415 SEGPTT--NPDEPVNEAQFMGAAK--------VKFKGQE---FELNDGACVIAAITSCTN 461

Query: 482 TSNPEVMLGAALLARNAVEKGLTSKPWVKTTIAPGSQVVNDYYDRSGLWPYLEKLGFYLV 541
           TSNP V+L A L+A+ A + G+  KPWVKT++APGS+VV DY +++GL   LE LGF LV
Sbjct: 462 TSNPSVILAAGLVAKKAKQLGINVKPWVKTSLAPGSKVVTDYLEKAGLMDDLESLGFNLV 521

Query: 542 GYGCTTCIGNSGPLPEEISKAVNDNDLSVTAVLSGNRNFEGRINPDVKMNYLASPPLVIA 601
           GYGCTTCIGNSGPL  EIS A+  + L V+++LSGNRNFEGRI+ DVKMN+LASPPLV+A
Sbjct: 522 GYGCTTCIGNSGPLATEISDAIQKHKLVVSSILSGNRNFEGRIHQDVKMNFLASPPLVVA 581

Query: 602 YALAGTMDFDFQTQPLGQDKDGKNVFLRDIWPSQQDVSDTIAAAINQEMFTRNYADVFKG 661
           YA+AG  D D   +PL QD +G +++L++IWPS ++VSD +   + +EMF ++YA+V++G
Sbjct: 582 YAIAGRTDIDVYNEPLAQDANGNDIYLKNIWPSVKEVSDLVKETVTKEMFEKSYANVYEG 641

Query: 662 DDRWRNLPTPSGNTFEWDPNSTYVRKPPYFEGMTAKPEPVGNISGARVLALLGDSVTTDH 721
           D RW+ +  P G  ++WD  STY++K P+F+GM  +P  +  I GAR LA LGDSVTTDH
Sbjct: 642 DSRWQQIKIPDGKLYDWDDASTYIKKAPFFDGMKVEPPGIPTIEGARCLAKLGDSVTTDH 701

Query: 722 ISPAGAIKPGTPAARYLDEHGVDRKDYNSFGSRRGNHEVMIRGTFANIRLRNQLLDDVSG 781
           ISPAGAIK   PA  YL E+GVD+  +NS+GSRRGNHEVM+RGTFAN+RL+N L     G
Sbjct: 702 ISPAGAIKADAPAGLYLQENGVDKAQFNSYGSRRGNHEVMMRGTFANVRLKNLLAPGTEG 761

Query: 782 GYTRDFTQPGGPQAFIYDAAQNYAAQHIPLVVFGGKEYGSGSSRDWAAKGTLLLGVRAVI 841
           G TR  TQPG     IYDAA  Y   + PL++  GKEYG+GSSRDWAAKG+LLLGV+AV+
Sbjct: 762 GVTR--TQPGDTLESIYDAAMEYQKNNTPLIILAGKEYGTGSSRDWAAKGSLLLGVKAVV 819

Query: 842 AESFERIHRSNLIGMGVIPLQFPEGKSASSLGLDGTEVFDITGIDVLNDGKTPKTVCVQA 901
           A+S+ERIHRSNLIGMGV+PLQF EG+S  S GL G E FDI G+    D      V V A
Sbjct: 820 AQSYERIHRSNLIGMGVLPLQFKEGESYESHGLTGQEQFDIDGLYDKTD-----EVTVIA 874

Query: 902 TKGDGATIEFDAVVRIDTPGEADYYRNGGILQYVLRNIL 940
           T  +G  +   A VRIDTP E DYY++GGILQYVLRN+L
Sbjct: 875 TNAEGKKVTLSADVRIDTPKEWDYYKHGGILQYVLRNML 913


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: 2319
Number of extensions: 113
Number of successful extensions: 6
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: 914
Length adjustment: 43
Effective length of query: 900
Effective length of database: 871
Effective search space:   783900
Effective search space used:   783900
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