Alignments for a candidate for acn in Thiohalospira halophila HL 3

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Thiohalospira halophila HL 3

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_093427176.1 BM272_RS02610 aconitate hydratase AcnA

Query= SwissProt::O53166
         (943 letters)



>NCBI__GCF_900112605.1:WP_093427176.1
          Length = 914

 Score = 1067 bits (2760), Expect = 0.0
 Identities = 543/942 (57%), Positives = 681/942 (72%), Gaps = 41/942 (4%)

Query: 7   NSFGAHDTLKVGEKSYQIYRLDAVPNTAKLPYSLKVLAENLLRNEDGSNITKDHIEAIAN 66
           +SF A   L+ G   Y+  RLDAVP + +LPYSLK+L ENLLR+EDG  +T + I+ +AN
Sbjct: 3   DSFQARAELEAGGNRYRYVRLDAVPGSERLPYSLKILLENLLRHEDGRTVTAEDIQRLAN 62

Query: 67  WDPKAEPSIEIQYTPARVVMQDFTGVPCIVDLATMREAIADLGGNPDKVNPLAPADLVID 126
           WDP+AEP+ EI + PARV+MQDFTGVP +VDLA MR+A+A+LGG+P+ +NPL PA+LVID
Sbjct: 63  WDPQAEPAHEIAFRPARVLMQDFTGVPAVVDLAAMRDAMAELGGDPEHINPLQPAELVID 122

Query: 127 HSVIADLFGRADAFERNVEIEYQRNGERYQFLRWGQGAFDDFKVVPPGTGIVHQVNIEYL 186
           HSV  D +G  +A+  N  +EYQRN ERY FL+WGQG+F +FK VPPG GIVHQ+N+E+L
Sbjct: 123 HSVQVDHYGNGEAYGLNEALEYQRNRERYTFLKWGQGSFANFKAVPPGKGIVHQINLEHL 182

Query: 187 ASVVMTRDGV-----AYPDTCVGTDSHTTMVNGLGVLGWGVGGIEAEAAMLGQPVSMLIP 241
             VV   +G      A+PDT VGTDSHT M+NGLGVLGWGVGGIEAEAAMLGQP+SML+P
Sbjct: 183 GRVVFGAEGPDGAQWAWPDTLVGTDSHTPMINGLGVLGWGVGGIEAEAAMLGQPISMLVP 242

Query: 242 RVVGFRLTGEIQPGVTATDVVLTVTEMLRQHGVVGKFVEFYGEGVAEVPLANRATLGNMS 301
           +VVGFRLTG++  G TATD+VLT+ E LR HGVVGKFVEF+G+G+ E+P+A+RAT+ NM+
Sbjct: 243 QVVGFRLTGQLPEGATATDLVLTIVEQLRAHGVVGKFVEFFGDGLDELPIADRATIANMA 302

Query: 302 PEFGSTAAIFPIDEETIKYLRFTGRTPEQVALVEAYAKAQGMWHDP-KHEPEFSEYLELN 360
           PE+G+T  IFP+D  T+ YLR TGR+ +QVA VEAYA+AQG++ +    E  ++  +EL+
Sbjct: 303 PEYGATCGIFPVDTATLDYLRLTGRSEDQVARVEAYARAQGLFRESGAPEAAYTSVVELD 362

Query: 361 LSDVVPSIAGPKRPQDRIALAQAKSTFREQIYHYVGNGSPDSPHDPHSKLDEVVEET--F 418
           L+ + PS+AGP+RPQDRIAL+QA+   RE                    LD ++ E    
Sbjct: 363 LATIEPSLAGPRRPQDRIALSQARRPIRES-------------------LDGILSERGMV 403

Query: 419 PASDPGQLTFANDDVATDETVHSAAAHADGRVSNPVRVKSDELGE-FVLDHGAVVIAAIT 477
           P  D     FA +   T   V     H         +V+ +  GE F LD G VVIAAIT
Sbjct: 404 PREDRETERFAAEGGHTAPGVEHQGDHRG-------KVRVERNGESFYLDDGMVVIAAIT 456

Query: 478 SCTNTSNPEVMLGAALLARNAVEKGLTSKPWVKTTIAPGSQVVNDYYDRSGLWPYLEKLG 537
           SCTNTSNP VMLGA LLA+ A+E+GL  KPWVKT++ PGS+VV DY + +GL   LE LG
Sbjct: 457 SCTNTSNPSVMLGAGLLAKKALERGLQVKPWVKTSLGPGSRVVTDYLEHAGLLDDLEGLG 516

Query: 538 FYLVGYGCTTCIGNSGPLPEEISKAVNDNDLSVTAVLSGNRNFEGRINPDVKMNYLASPP 597
           F +VGYGCTTCIGNSGPL E IS A+ ++DL V ++LSGNRNFEGRI+ +V+MNYLASPP
Sbjct: 517 FDVVGYGCTTCIGNSGPLDESISHAIREDDLVVCSILSGNRNFEGRIHSEVRMNYLASPP 576

Query: 598 LVIAYALAGTMDFDFQTQPLGQDKDGKNVFLRDIWPSQQDVSDTIAAAINQEMFTRNYAD 657
           LV+AYALAG MD D     LG D DG  V+LRDIWPSQ ++   +   +  + F + YAD
Sbjct: 577 LVVAYALAGRMDIDPYNDALGTDADGNAVYLRDIWPSQAEIQALVRDHVRADAFEQAYAD 636

Query: 658 VFKGDDRWRNLPTPSGNTFEWDPNSTYVRKPPYFEGMTAKPEPVGNISGARVLALLGDSV 717
           VF G +RW  L  P G  ++W  +STY+R+PP+FEG+  +PEPVG+I+GAR LA++GDSV
Sbjct: 637 VFAGGERWEALTAPGGRLYDWAEDSTYIRRPPFFEGIQPEPEPVGDITGARALAVVGDSV 696

Query: 718 TTDHISPAGAIKPGTPAARYLDEHGVDRKDYNSFGSRRGNHEVMIRGTFANIRLRNQLLD 777
           TTDHISPAG+I   +PA  YL E+GV+  ++NS+G+RRGNHEVM+RGTFAN R RN+L  
Sbjct: 697 TTDHISPAGSIAADSPAGHYLRENGVEPAEFNSYGARRGNHEVMMRGTFANPRFRNRLAP 756

Query: 778 DVSGGYTRDFTQPGGPQAFIYDAAQNYAAQHIPLVVFGGKEYGSGSSRDWAAKGTLLLGV 837
           D  GG+T    QP G    IYDAA  YA +  PLVV  GKEYGSGSSRDWAAKG  LLGV
Sbjct: 757 DTEGGWTAH--QPSGKVMPIYDAAMRYAEEGTPLVVLAGKEYGSGSSRDWAAKGPRLLGV 814

Query: 838 RAVIAESFERIHRSNLIGMGVIPLQFPEGKSASSLGLDGTEVFDITGIDVLNDGKTPKTV 897
           RAVIAES+ERIHRSNL+GMG++PLQF +G +A SLGLDGTE F + G   L DG   + V
Sbjct: 815 RAVIAESYERIHRSNLVGMGILPLQFRDGDTADSLGLDGTETFALAG---LGDGSADQ-V 870

Query: 898 CVQATKGDGATIEFDAVVRIDTPGEADYYRNGGILQYVLRNI 939
            V AT  DG    F A VRIDTP E +YYR+GGIL YVLR +
Sbjct: 871 TVTATTADGGETTFTARVRIDTPQEVEYYRHGGILPYVLRQL 912


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: 2554
Number of extensions: 130
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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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