GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acnD in Halomonas xinjiangensis TRM 0175

Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate WP_043529276.1 JH15_RS08095 aconitate hydratase AcnA

Query= BRENDA::Q8EJW3
         (867 letters)



>NCBI__GCF_000759345.1:WP_043529276.1
          Length = 914

 Score =  721 bits (1862), Expect = 0.0
 Identities = 400/896 (44%), Positives = 543/896 (60%), Gaps = 75/896 (8%)

Query: 20  YFDTREAIEAIAPGAYAKLPYTSRVLAENLVRRCEPEMLTASLKQII-----ESKQELDF 74
           Y+   +A EA+  G   +LP T ++L EN +R  + E ++    Q +     E++   + 
Sbjct: 22  YYSLPKAAEAL--GDIQRLPVTLKILLENQLRFADDESVSREDMQALVDWQQEARSTREI 79

Query: 75  PWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDHSLAVEYGGFD 134
            + PARV+  D  G   +VDLA +R A+   G DP+++NP+ P  L++DHS+ V+  G D
Sbjct: 80  GYRPARVLMQDFTGVPGVVDLASMRAAVEKLGEDPSRINPLSPVDLVIDHSVMVDKYG-D 138

Query: 135 KDAFAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQINLERMSPVIHARN-- 192
             AF  N AIE  RN +R+ F+ W Q AF N  V+P G GI HQ+NLE +   +  +   
Sbjct: 139 PSAFRDNVAIEMDRNRERYEFLRWGQDAFDNFRVVPPGTGICHQVNLEYLGKTVWVKEED 198

Query: 193 --GVAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGVELTGKP 250
               A+PDTLVGTDSHT  ++ LGV+  GVGG+EAE+ MLG+   M +P+++G +LTGK 
Sbjct: 199 GKSFAYPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQPVSMLIPEVVGFKLTGKL 258

Query: 251 QPGITATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGATAAMFY 310
           + GITATD+VL +T+ LR + VV  ++EF+G+G + L L DRATI+NM PE+GAT   F 
Sbjct: 259 REGITATDLVLTVTQMLRQKGVVGKFVEFYGDGLDDLPLADRATIANMAPEYGATCGFFP 318

Query: 311 IDQQTLDYLTLTGREAEQVKLVETYAKTAGLWSDDLKQAVYPRTLHFDLSSVVRTIAGPS 370
           +D +TL+YL LTGR  E+V LVE Y K   LW     + V+  TL  D+  V  ++AGP 
Sbjct: 319 VDDETLNYLRLTGRSDEEVALVEAYCKEQDLWRKPGAEPVFSDTLQLDMGDVEASLAGPK 378

Query: 371 NPHARVPTSEL--------------AARGISGEVENEPGLMP------------------ 398
            P  RV  S++              A+    G+ ++E G MP                  
Sbjct: 379 RPQDRVALSDMKSTFENLMGDDAAEASATARGKFDSEGGQMPVGTHEHFEHHDSQDVDVE 438

Query: 399 -------DGAVIIAAITSCTNTSNPRNVIAAGLLARNANAKGLTRKPWVKTSLAPGSKAV 451
                   GAV+IAAITSCTNTSNP  ++AAGLLAR A  KGL  KPWVKTSLAPGSK V
Sbjct: 439 GSTFKLNPGAVVIAAITSCTNTSNPSVMMAAGLLARKAVEKGLDTKPWVKTSLAPGSKVV 498

Query: 452 QLYLEEANLLPELESLGFGIVGFACTTCNGMSGALDPVIQQEVIDRDLYATAVLSGNRNF 511
             YL       +L +LGF +VG+ CTTC G SG L P I++ + D DL   +VLSGNRNF
Sbjct: 499 TDYLAAGGFQDDLNALGFNLVGYGCTTCIGNSGPLLPPIEKAIEDGDLTVASVLSGNRNF 558

Query: 512 DGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIEKDVLGLDKDGKPVRLINIWPSDAEIDA 571
           +GR+HP  K  +LASPPLVVAYA+AG +R DI K+ LG  KDGKPV L +IWPS AEI A
Sbjct: 559 EGRVHPLVKTNWLASPPLVVAYALAGNVRLDISKEPLGEGKDGKPVYLQDIWPSQAEI-A 617

Query: 572 VIAASVKPEQFRKVYEPMFDLSVDYGDKV--------SPLYDWRPQSTYIRRPPYWEGAL 623
                V+ E +RK Y  +F+     GD+V        S +Y W   STYI+ PP++EG  
Sbjct: 618 EAVEKVRTEMYRKEYAEVFE-----GDEVWKAIDVPQSQVYQWSEDSTYIQHPPFFEGMG 672

Query: 624 AGERTLKGM---RPLAVLGDNITTDHLSPSNAIMMDSAAGEYLHKMGLPEEDFNSYATHR 680
                L+ +   R LA+LGD++TTDH+SP+ AI  DS AG YL + G+   DFNSY + R
Sbjct: 673 REPEPLQDVENARVLAMLGDSVTTDHISPAGAIKPDSPAGRYLQEHGVKPMDFNSYGSRR 732

Query: 681 GDHLTAQRATFANPKLKNEMAIVDGKVKQGSLARIEPEGIVTRMWEAIETYMDRKQPLII 740
           G+H    R TFAN +++NEM  +DG   +G   R  P      +++A   Y +  +PL++
Sbjct: 733 GNHEVMMRGTFANVRIRNEM--LDG--VEGGYTRHVPSDEQMAIYDAAMKYAEEGRPLVV 788

Query: 741 IAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTNLVGMGVLPLEFKAGENRATYG 800
           IAG +YG GSSRDWAAKG RL GV A++AE +ERIHR+NL+GMGV+PL+F  GE+R + G
Sbjct: 789 IAGKEYGTGSSRDWAAKGTRLLGVRAVLAESYERIHRSNLIGMGVVPLQFPEGEDRKSLG 848

Query: 801 IDGTE--VFDVIGSIAPRADLTVIITRKNGERVEVPVTCRLDTAEEVSIYEAGGVL 854
           + G E    D I  + P   + V I    GE+ ++   CR+DTA E+  Y  GG+L
Sbjct: 849 LTGDEEVSIDGIADLTPGGQVNVTIKSDKGEK-KIEALCRIDTANELEYYRHGGIL 903


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: 1994
Number of extensions: 91
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: 867
Length of database: 914
Length adjustment: 43
Effective length of query: 824
Effective length of database: 871
Effective search space:   717704
Effective search space used:   717704
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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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:

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:

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:

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:

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