Alignments for a candidate for acnD in Halomonas desiderata SP1

GapMind for catabolism of small carbon sources

Alignments for a candidate for acnD in Halomonas desiderata SP1

Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate WP_086509356.1 BZY95_RS07660 aconitate hydratase AcnA

Query= BRENDA::Q8EJW3
         (867 letters)



>NCBI__GCF_002151265.1:WP_086509356.1
          Length = 916

 Score =  733 bits (1893), Expect = 0.0
 Identities = 400/903 (44%), Positives = 554/903 (61%), Gaps = 77/903 (8%)

Query: 15  GTALDYFDTREAIEAIAPGAYAKLPYTSRVLAENLVRRCE-PEMLTASLKQIIESKQ--- 70
           GT   Y+   +  E +  G   +LP T ++L EN +R  + P +    ++ +I+ +Q   
Sbjct: 17  GTTYHYYSLPKVAEEM--GNIDRLPKTLKILLENQLRFADDPSVAREDIQALIDWQQGGR 74

Query: 71  -ELDFPWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDHSLAVE 129
              +  + PARV+  D  G   +VDLA +R A+   G DP+++NP+ P  L++DHS+ V+
Sbjct: 75  SNREIGYRPARVLMQDFTGVPGVVDLASMRAAVEKLGEDPSRINPLSPVDLVIDHSVMVD 134

Query: 130 YGGFDKDAFAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQINLERMSPVIH 189
             G +  AF  N AIE  RN +R+ F+ W Q+AF N  V+P G GI HQ+NLE +   + 
Sbjct: 135 KFG-NPTAFKDNVAIEMERNRERYEFLRWGQQAFDNFSVVPPGTGICHQVNLEYLGRTVW 193

Query: 190 AR--NG--VAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGVE 245
            +  NG   A+PDTLVGTDSHT  ++ LGV+  GVGG+EAE+ MLG+   M +P+++G +
Sbjct: 194 TKEENGKVFAYPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQPVSMLIPEVVGFK 253

Query: 246 LTGKPQPGITATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGAT 305
           LTGK + GITATD+VL +T+ LR++ VV  ++EF+G+G   L L DRATI+NM PE+GAT
Sbjct: 254 LTGKLKEGITATDLVLTVTQMLRSRGVVGKFVEFYGDGLADLPLADRATIANMAPEYGAT 313

Query: 306 AAMFYIDQQTLDYLTLTGREAEQVKLVETYAKTAGLWSDDLKQAVYPRTLHFDLSSVVRT 365
              F +D +TL YL LTGRE   + LV+ Y K  GLW +   + ++  TLH DL  V  +
Sbjct: 314 CGFFPVDDETLAYLRLTGREDSLIALVKEYCKAQGLWREPGDEPIFSDTLHLDLGDVEAS 373

Query: 366 IAGPSNPHARVPTSEL-------------------------------AARGISG------ 388
           +AGP  P  RV   ++                                A G+        
Sbjct: 374 LAGPKRPQDRVALKDMKTTFEKLMQGEENGKATPSEEKGRLFSEGGQTAVGVHDSYEHHD 433

Query: 389 ----EVENEPGLMPDGAVIIAAITSCTNTSNPRNVIAAGLLARNANAKGLTRKPWVKTSL 444
               E++ E   +  GAV+IAAITSCTNTSNP  ++AAGLLARNA AKGLT KPWVKTSL
Sbjct: 434 SQNVEMDGEQFKLNPGAVVIAAITSCTNTSNPSVMLAAGLLARNARAKGLTTKPWVKTSL 493

Query: 445 APGSKAVQLYLEEANLLPELESLGFGIVGFACTTCNGMSGALDPVIQQEVIDRDLYATAV 504
           APGSK V  YL   ++  +L++LGF +VG+ CTTC G SG L P I++ V D DL   +V
Sbjct: 494 APGSKVVTEYLAAGSVQDDLDALGFNLVGYGCTTCIGNSGPLPPPIEKAVEDGDLTVASV 553

Query: 505 LSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIEKDVLGLDKDGKPVRLINIWP 564
           LSGNRNF+GRIHP  K  +LASPPLVVAYA+AG +R D+ +D LG D+DG PV L +IWP
Sbjct: 554 LSGNRNFEGRIHPLVKTNWLASPPLVVAYALAGNVRLDLTQDPLGEDQDGNPVYLQDIWP 613

Query: 565 SDAEIDAVIAASVKPEQFRKVYEPMFDLSVDYGDKV--------SPLYDWRPQSTYIRRP 616
           S A+I + +   VK E FRK Y  +F+     GD+         S +Y+W P STYI+ P
Sbjct: 614 SQADIASAV-EKVKTEMFRKEYAEVFE-----GDETWKALQVPQSQVYEWSPSSTYIQHP 667

Query: 617 PYWEGALAGERTLKGMRP---LAVLGDNITTDHLSPSNAIMMDSAAGEYLHKMGLPEEDF 673
           P++EG       ++ +R    LA+LGD++TTDH+SP+ +I  DS AG YL + G+   DF
Sbjct: 668 PFFEGMGRDPEPIEDVRDAHILAILGDSVTTDHISPAGSIKPDSPAGRYLQERGIKPVDF 727

Query: 674 NSYATHRGDHLTAQRATFANPKLKNEMAIVDGKVKQGSLARIEPEGIVTRMWEAIETYMD 733
           NSY + RG+H    R TFAN +++NEM  +DG V  G   R  P G    +++A   Y +
Sbjct: 728 NSYGSRRGNHEVMMRGTFANVRIRNEM--LDGVV--GGETRHVPTGEQMAIYDAAMKYQE 783

Query: 734 RKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTNLVGMGVLPLEFKAG 793
           +  PL+++AG +YG GSSRDWAAKG RL GV A++AE +ERIHR+NL+GMGV+PL+F  G
Sbjct: 784 KGTPLVVVAGKEYGTGSSRDWAAKGTRLLGVRAVLAESYERIHRSNLIGMGVVPLQFPEG 843

Query: 794 ENRATYGIDGTEVFDVIG--SIAPRADLTVIITRKNGERVEVPVTCRLDTAEEVSIYEAG 851
           ENR T G+ G E   + G   + P   + V +    GE+ ++   CR+DTA E+  Y  G
Sbjct: 844 ENRKTLGLTGDETISIEGLADLTPGGQVNVTVKSAKGEK-KIEALCRIDTANELEYYRHG 902

Query: 852 GVL 854
           G+L
Sbjct: 903 GIL 905


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: 1998
Number of extensions: 86
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: 916
Length adjustment: 43
Effective length of query: 824
Effective length of database: 873
Effective search space:   719352
Effective search space used:   719352
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