Alignments for a candidate for acn in Thioalkalivibrio paradoxus ARh 1

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Thioalkalivibrio paradoxus ARh 1

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_006747496.1 THITH_RS08500 aconitate hydratase AcnA

Query= SwissProt::O53166
         (943 letters)



>NCBI__GCF_000227685.2:WP_006747496.1
          Length = 916

 Score = 1066 bits (2757), Expect = 0.0
 Identities = 550/933 (58%), Positives = 676/933 (72%), Gaps = 36/933 (3%)

Query: 14  TLKVGEKSYQIYRLDAVPNTAKLPYSLKVLAENLLRNEDGSNITKDHIEAIANWDPKAEP 73
           TLK G +   I  +      A LPYSLK+L ENLLR EDG  + +  IEA+ +W+P+AEP
Sbjct: 11  TLKAGGRECAIVPITDDARAASLPYSLKILLENLLRFEDGRTVRRSDIEALLDWNPQAEP 70

Query: 74  SIEIQYTPARVVMQDFTGVPCIVDLATMREAIADLGGNPDKVNPLAPADLVIDHSVIADL 133
           + EI + PARV++QDFTGVP +VDLA MR+A+  LGG+P K+NP+ PA+LVIDHSV  D 
Sbjct: 71  AQEIAFRPARVLLQDFTGVPAVVDLAAMRDAMEALGGDPAKINPMQPAELVIDHSVQVDA 130

Query: 134 FGRADAFERNVEIEYQRNGERYQFLRWGQGAFDDFKVVPPGTGIVHQVNIEYLASVVMTR 193
            G  +A   N E+EY RN ERY FL+WGQ AF +FKVVPP TGIVHQVN+E+LA  V   
Sbjct: 131 HGNVNALNLNAELEYSRNRERYSFLKWGQQAFHNFKVVPPDTGIVHQVNLEFLARTVFLD 190

Query: 194 DGV-----AYPDTCVGTDSHTTMVNGLGVLGWGVGGIEAEAAMLGQPVSMLIPRVVGFRL 248
           DG      AYPDT VGTDSHTTMVNGLGVLGWGVGGIEAEAAMLGQP+SMLIP+VVGFRL
Sbjct: 191 DGPDGRCRAYPDTLVGTDSHTTMVNGLGVLGWGVGGIEAEAAMLGQPISMLIPQVVGFRL 250

Query: 249 TGEIQPGVTATDVVLTVTEMLRQHGVVGKFVEFYGEGVAEVPLANRATLGNMSPEFGSTA 308
           TG +  G TATD+VL + EMLR+HGVVGKFVEF+GEG+A++PLA+RAT+ NM+PE+G+T 
Sbjct: 251 TGRLSEGATATDLVLVIVEMLRRHGVVGKFVEFFGEGLAQLPLADRATIANMAPEYGATC 310

Query: 309 AIFPIDEETIKYLRFTGRTPEQVALVEAYAKAQGMWHDPKHEP-EFSEYLELNLSDVVPS 367
            IFPID ET++YLR TGR P  V L+EAYA+AQG+W D    P  +++ LEL+L  V PS
Sbjct: 311 GIFPIDGETLEYLRLTGRDPGHVELIEAYARAQGLWRDDSAPPARYTDVLELDLGTVEPS 370

Query: 368 IAGPKRPQDRIALAQAKSTFREQIYHYVGNGSPDSPHDPHSKLDEVVEETFPASDPGQLT 427
           +AGP+RPQDR+ L +A     +++  ++G           S L E  E TF  S+P    
Sbjct: 371 LAGPRRPQDRLRLGEAG----KRVGEFIG-----------SMLKER-ESTF--SEP---- 408

Query: 428 FANDDVATDETVHSAAAHADGRVSNPVRVKSDELGE-FVLDHGAVVIAAITSCTNTSNPE 486
            A  +    E  H+A        + P R      GE FVLDHG +VIAAITSCTNTSNP 
Sbjct: 409 -AEAERFEAEGGHTAVGVEHQAEATPKRSNVTMNGEEFVLDHGDIVIAAITSCTNTSNPS 467

Query: 487 VMLGAALLARNAVEKGLTSKPWVKTTIAPGSQVVNDYYDRSGLWPYLEKLGFYLVGYGCT 546
           VMLGA L+AR A E+GL  KPWVKT++APGS+VV +Y   SGL   LE LGF++VGYGCT
Sbjct: 468 VMLGAGLVARKARERGLKVKPWVKTSLAPGSKVVTEYLQHSGLLDDLEALGFHVVGYGCT 527

Query: 547 TCIGNSGPLPEEISKAVNDNDLSVTAVLSGNRNFEGRINPDVKMNYLASPPLVIAYALAG 606
           TCIGNSGPLP+ IS+AV  +DL V++VLSGNRNFEGRI+ +V+MN+LASPPLV+AYALAG
Sbjct: 528 TCIGNSGPLPDPISEAVLKDDLIVSSVLSGNRNFEGRIHSEVRMNFLASPPLVVAYALAG 587

Query: 607 TMDFDFQTQPLGQDKDGKNVFLRDIWPSQQDVSDTIAAAINQEMFTRNYADVFKGDDRWR 666
           TM  D    P+GQD+ G+ V+L+D+WPS  ++   + A++  + FT  Y DV++G+DRW 
Sbjct: 588 TMATDLLNDPIGQDEQGQPVYLKDVWPSNAEIQAMVTASVTAKSFTEAYRDVYRGEDRWM 647

Query: 667 NLPTPSGNTFEWDPNSTYVRKPPYFEGMTAKPEPVGNISGARVLALLGDSVTTDHISPAG 726
            L  P G  FEW  +STYVR PPYF GMT  P P+  I  ARVLALLGDSVTTDHISPAG
Sbjct: 648 RLAAPEGERFEWTEDSTYVRNPPYFTGMTMTPAPLTEIRDARVLALLGDSVTTDHISPAG 707

Query: 727 AIKPGTPAARYLDEHGVDRKDYNSFGSRRGNHEVMIRGTFANIRLRNQLLDDVSGGYTRD 786
           AI+P +PA +YL   GV   D+NS+GSRRGNHEVM+RGTFAN+RLRN L     GG T  
Sbjct: 708 AIRPDSPAGKYLASQGVKTADFNSYGSRRGNHEVMMRGTFANVRLRNLLAPGTEGGVTLH 767

Query: 787 FTQPGGPQAFIYDAAQNYAAQHIPLVVFGGKEYGSGSSRDWAAKGTLLLGVRAVIAESFE 846
              P G Q  IYDAA  Y  +++PL+V  GKEYG+GSSRDWAAKGT+LLGVRAVI ESFE
Sbjct: 768 L--PAGEQMPIYDAAIRYQQENVPLIVIAGKEYGTGSSRDWAAKGTMLLGVRAVIVESFE 825

Query: 847 RIHRSNLIGMGVIPLQFPEGKSASSLGLDGTEVFDITGIDVLNDGKTPKTVCVQATKGDG 906
           RIHRSNLIGMGV+PLQF  G++A SLGL G E + I G+D   +G+  + V V+A + DG
Sbjct: 826 RIHRSNLIGMGVLPLQFLPGENAESLGLTGRETYSIEGLD---EGRAAE-VTVRARRDDG 881

Query: 907 ATIEFDAVVRIDTPGEADYYRNGGILQYVLRNI 939
           +   F A VRIDTP E DY+R+GGIL YVLR +
Sbjct: 882 SEHRFQARVRIDTPQEVDYFRHGGILPYVLRQL 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: 2299
Number of extensions: 88
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: 916
Length adjustment: 43
Effective length of query: 900
Effective length of database: 873
Effective search space:   785700
Effective search space used:   785700
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 Apr 09 2024. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
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Protein sequences (fasta format)
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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