Alignments for a candidate for acnD in Halomonas stevensii S18214

GapMind for catabolism of small carbon sources

Alignments for a candidate for acnD in Halomonas stevensii S18214

Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate WP_016916040.1 HSS18214_RS0114705 aconitate hydratase AcnA

Query= BRENDA::Q8EJW3
         (867 letters)



>NCBI__GCF_000275725.1:WP_016916040.1
          Length = 915

 Score =  716 bits (1849), Expect = 0.0
 Identities = 401/919 (43%), Positives = 552/919 (60%), Gaps = 80/919 (8%)

Query: 1   MSTVMNTQYRKPLPGTALDYFDTREAIEAIAPGAYAKLPYTSRVLAENLVRRCEPEMLTA 60
           MS + +T +          Y+   +A E +  G   +LP T ++L EN +R  + E +  
Sbjct: 1   MSKIPSTLHTLTAGSQEYHYYSLPKAAETL--GNIDRLPKTLKILLENQLRFADDESVEQ 58

Query: 61  SLKQII-----ESKQELDFPWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPV 115
           +  Q +     E +   +  + PARV+  D  G   +VDLA +R A+ + G DPA++NP+
Sbjct: 59  ADMQALVDWQNEGQSSREIGYRPARVLMQDFTGVPGVVDLASMRAAVESLGEDPARINPL 118

Query: 116 VPTQLIVDHSLAVEYGGFDKDAFAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGI 175
            P  L++DHS+ V+  G    AF +N  IE +RN +R+ F+ W QKAF N  V+P G GI
Sbjct: 119 SPVDLVIDHSVMVDKFG-TPTAFQENVDIEMQRNGERYEFLRWGQKAFDNFSVVPPGTGI 177

Query: 176 MHQINLERMSPVIHARNG----VAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLG 231
            HQ+NLE +   +  +       A+PDTLVGTDSHT  ++ LGV+  GVGG+EAE+ MLG
Sbjct: 178 CHQVNLEYLGRTVWTKQEDGKTFAYPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLG 237

Query: 232 RASYMRLPDIIGVELTGKPQPGITATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGD 291
           +   M +P++IG +LTGK Q GITATD+VL +TE LR + VV  ++EF+G+G + L L D
Sbjct: 238 QPVSMLIPEVIGFKLTGKLQEGITATDLVLTVTEMLRKKGVVGKFVEFYGDGLKDLPLAD 297

Query: 292 RATISNMTPEFGATAAMFYIDQQTLDYLTLTGREAEQVKLVETYAKTAGLWSDDLKQAVY 351
           RATI+NM PE+GAT   F +D +TL+YL LTGRE E V LVE Y+K  GLW +   + ++
Sbjct: 298 RATIANMAPEYGATCGFFPVDDETLNYLRLTGREDELVALVEAYSKAQGLWREPGDEPIF 357

Query: 352 PRTLHFDLSSVVRTIAGPSNPHARVPTSELAARGIS--------------GEVENEPGL- 396
             TL  D+SSV  ++AGP  P  RV    +     S              G++ +E G  
Sbjct: 358 TDTLSLDMSSVEASLAGPKRPQDRVSLKNMPKAFASVMEEDGKSYPATETGKLSSEGGQT 417

Query: 397 ----------------------------MPDGAVIIAAITSCTNTSNPRNVIAAGLLARN 428
                                       +  GAV+IAAITSCTNTSNP  ++AAGLLARN
Sbjct: 418 AVGIDRSFERAFQHNDSQAVKMGEQDFNLDPGAVVIAAITSCTNTSNPSVMMAAGLLARN 477

Query: 429 ANAKGLTRKPWVKTSLAPGSKAVQLYLEEANLLPELESLGFGIVGFACTTCNGMSGALDP 488
           A  KGL  KPWVKTSLAPGSK V  YL  A L  +L++LGF +VG+ CTTC G SG L  
Sbjct: 478 ARQKGLATKPWVKTSLAPGSKVVTDYLAAAELNDDLDALGFNLVGYGCTTCIGNSGPLPD 537

Query: 489 VIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIEKDVL 548
            I++ +   DL   +VLSGNRNF+GR+HP  K  +LASPPLVVAYA+AG ++ ++  D L
Sbjct: 538 AIEKAIQQGDLAVASVLSGNRNFEGRVHPLVKTNWLASPPLVVAYALAGNVQCNLSTDPL 597

Query: 549 GLDKDGKPVRLINIWPSDAEIDAVIAASVKPEQFRKVYEPMFDLSVDYGDKV-------- 600
           G D DG PV L +IWPS A+I A     V  E FRK Y  +F+     GD+         
Sbjct: 598 GEDSDGNPVYLKDIWPSQADI-ANAVQKVNTEMFRKEYSAVFE-----GDETWQSIKVPE 651

Query: 601 SPLYDWRPQSTYIRRPPYWEGALA---GERTLKGMRPLAVLGDNITTDHLSPSNAIMMDS 657
           S +Y+W P STYI+ PP+++G          ++  R LA+LGD++TTDH+SP+ +I  DS
Sbjct: 652 SNVYEW-PSSTYIQHPPFFKGMQREPDAIEDIQSARVLAILGDSVTTDHISPAGSIKPDS 710

Query: 658 AAGEYLHKMGLPEEDFNSYATHRGDHLTAQRATFANPKLKNEMAIVDGKVKQGSLARIEP 717
            AG YL + G+   DFNSY + RG+H    R TFAN ++KNEM  +DG V  G   R  P
Sbjct: 711 PAGRYLQEHGVKPVDFNSYGSRRGNHEVMMRGTFANVRIKNEM--LDGVV--GGETRHVP 766

Query: 718 EGIVTRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHR 777
            G    +++A   Y +   PL+++AG +YG GSSRDWAAKG RL GV A++AE +ERIHR
Sbjct: 767 SGEQMSIYDAAMKYKEEGTPLVVVAGKEYGTGSSRDWAAKGTRLLGVRAVIAESYERIHR 826

Query: 778 TNLVGMGVLPLEFKAGENRATYGIDGTEVFDVIG--SIAPRADLTVIITRKNGERVEVPV 835
           +NL+GMGV+PL+F  GE+R + G+ G E   + G   ++P   + V+I + + ER  V  
Sbjct: 827 SNLIGMGVVPLQFPEGESRTSLGLTGDEEISIAGLNDLSPGGTVKVVIKQGDQERT-VDA 885

Query: 836 TCRLDTAEEVSIYEAGGVL 854
            CR+DTA E++ Y  GG+L
Sbjct: 886 KCRIDTANELAYYRHGGIL 904


Lambda     K      H
   0.318    0.136    0.397 

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: 1983
Number of extensions: 97
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 867
Length of database: 915
Length adjustment: 43
Effective length of query: 824
Effective length of database: 872
Effective search space:   718528
Effective search space used:   718528
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 (21.7 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 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