Alignments for a candidate for acnD in Algoriphagus aquaeductus T4

GapMind for catabolism of small carbon sources

Alignments for a candidate for acnD in Algoriphagus aquaeductus T4

Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate WP_111391081.1 CLV31_RS01395 aconitate hydratase

Query= BRENDA::Q8EJW3
         (867 letters)



>NCBI__GCF_003253485.1:WP_111391081.1
          Length = 753

 Score =  205 bits (521), Expect = 9e-57
 Identities = 226/800 (28%), Positives = 351/800 (43%), Gaps = 121/800 (15%)

Query: 69  KQELDFPWFPARVVCHDILGQTALVDL--AGLRDAIAAKGGDPAQVNPVVPTQLIVDHSL 126
           K  +DF   P RV   D   Q AL+    AG R+ +A            VP+ +  DH +
Sbjct: 54  KSYVDFQ--PDRVAMQDATAQMALLQFMQAG-REKVA------------VPSTVHCDHLI 98

Query: 127 AVEYGGFDKDAFAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQINLERMSP 186
             E G  +KD    N+A +  +N + + F+      +  I     G GI+HQ+ LE    
Sbjct: 99  QAEVGA-EKDL---NKAKD--KNREVYDFLASVSNKY-GIGFWKPGAGIIHQVVLENY-- 149

Query: 187 VIHARNGVAFPD-TLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGVE 245
                   AFP   ++GTDSHTP+   LG+IAIGVGG +A  VM G    ++ P +IGV+
Sbjct: 150 --------AFPGGMMIGTDSHTPNAGGLGMIAIGVGGADACDVMAGLPWELKFPKLIGVK 201

Query: 246 LTGKPQPGITATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGAT 305
           LTGK     +A D++L +   L  +    + +E+FGEGA +L+   + TI NM  E GAT
Sbjct: 202 LTGKMSGWTSAKDVILKVAGILTVKGGTGAIVEYFGEGARSLSATGKGTICNMGAEIGAT 261

Query: 306 AAMFYIDQQTLDYLTLTGREAEQVKLVETYAKTAGLWSDDLKQA----VYPRTLHFDLSS 361
            ++F  D+++  YL  TGR A+   + +  A+   L  D+   A     + + +  +LS 
Sbjct: 262 TSIFGYDEKSAAYLQGTGR-ADIAAMADAIAE--HLTGDEEVYANPEQYFDQLIEINLSE 318

Query: 362 VVRTIAGPSNPHARVPTSELAARGISGEVENEPGLMPDGAVIIAAITSCTNTSNPRNVIA 421
           +   + GP  P    P S+ AA         E G      + +  I SCTN+S   ++  
Sbjct: 319 LEPHVNGPFTPDLAWPISKFAA------AVKENGW--PAKLDVGLIGSCTNSSY-EDISR 369

Query: 422 AGLLARNANAKGLTRKPWVKTSLAPGSKAVQLYLEEANLLPELESLGFGIVGFACTTCNG 481
           A  LA+ A  K L  K   + ++ PGS+ V+  +E    L     +G  ++  AC  C G
Sbjct: 370 AASLAQQAVDKKLNAKS--EYTITPGSEQVRFTVERDGFLDTFGKMGGVVLANACGPCIG 427

Query: 482 MSGALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAK-QAFLASPPLVVAYAIAGTIR 540
                    Q++        + + S NRNF  R        AF+ASP +V A AIAG + 
Sbjct: 428 QWARHGAEKQEK-------NSIITSFNRNFAKRADGNPNTHAFVASPEIVTALAIAGDLT 480

Query: 541 FDIEKDVLGLDKDGKPVRLINIWPSDAEIDAVIAASVKPEQFRKVYEPMFDLSVDYGDKV 600
           F+   D L  + +G+ V+L    P   E+         P +   V +  +    + G  V
Sbjct: 481 FNPLTDTL-TNAEGQQVKLDE--PRGLEL---------PTKGFAVEDAGYQAPAEDGSSV 528

Query: 601 SPLYDWRPQSTYIR---RPPYWEGALAGERTLKGMRPLAVLGDNITTDHLSPSNAIMMDS 657
             L    P S  ++     P WEG       L G++ L       TTDH+         S
Sbjct: 529 QVLVS--PTSDRLQLLDSFPAWEGT-----DLTGLKLLIKAKGKCTTDHI---------S 572

Query: 658 AAGEYLHKMGLPEEDFNSYATHRGDHLTAQRATFANPKLKNEMAIVDGKVKQGSLARIEP 717
            AG +L   G  +   N+                A   +KN++    G+V   +  + + 
Sbjct: 573 MAGPWLKYRGHLDNISNNMLIG-----AVNAFNDATNSVKNQLTGEYGEV-PATQRQYKA 626

Query: 718 EGIVTRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHR 777
            GI +                I++   +YG+GSSR+ AA   R  GV AI+ + F RIH 
Sbjct: 627 AGIGS----------------IVVGDENYGEGSSREHAAMEPRFLGVRAILVKSFARIHE 670

Query: 778 TNLVGMGVLPLEFKAGENRATYG-IDGTEVFDVIG--SIAPRADLTVIITRKNGERVEVP 834
           TNL   G+L L F    N + Y  I   +  D++G  S AP   L +++  ++G    + 
Sbjct: 671 TNLKKQGMLALTF---ANPSDYDLIQENDSIDIVGLTSFAPGKPLQIVLNHQDGSSHSIQ 727

Query: 835 VTCRLDTAEEVSIYEAGGVL 854
                +   ++  ++AG  L
Sbjct: 728 ANHTYNEG-QIEWFKAGSAL 746


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: 1515
Number of extensions: 90
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 2
Length of query: 867
Length of database: 753
Length adjustment: 41
Effective length of query: 826
Effective length of database: 712
Effective search space:   588112
Effective search space used:   588112
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:

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