Alignments for a candidate for aacS in Marinobacter adhaerens HP15

GapMind for catabolism of small carbon sources

Alignments for a candidate for aacS in Marinobacter adhaerens HP15

Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate GFF1020 HP15_999 acyl-CoA synthase

Query= reanno::acidovorax_3H11:Ac3H11_3009
         (578 letters)



>FitnessBrowser__Marino:GFF1020
          Length = 548

 Score =  645 bits (1663), Expect = 0.0
 Identities = 317/553 (57%), Positives = 399/553 (72%), Gaps = 7/553 (1%)

Query: 24  VPLIEQTIGAFFADMVARQPEREALVSVHQGRRYTYAQLQTEAHRLASALLGMGLTPGDR 83
           +PL+  TIG        + P+ EALV +HQ  R+TY +   +    A A + +G+  GDR
Sbjct: 1   MPLLGMTIGEMLDRTAEKYPDNEALVCLHQDIRWTYKEFVEKVDEAARAFMAIGVKRGDR 60

Query: 84  VGIWSHNNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSMARFKTSDY 143
           VGIWS N  EW + Q ATA+VG +LVNINPAY   E++YALN  G   LV+   FK S+Y
Sbjct: 61  VGIWSPNRYEWTVTQFATAKVGAILVNINPAYGVHELQYALNLAGITTLVTADSFKASNY 120

Query: 144 LGMLRELAPEWQGQQPGHLQAAKLPQLKTVVWIDDEAGQGADEPGLLRFTELIA-RGNAA 202
             M+ ELAPE +   PG L+A  +P+L+ V+ + ++        G+  + E +    + +
Sbjct: 121 REMIYELAPELKRSSPGKLKADHVPELRAVINVHEDK-----HDGMWTWKEFLGFSSDVS 175

Query: 203 DPRLAQVAAGLQATDPINIQFTSGTTGFPKGATLTHRNILNNGFFIGECMKLTPADRLCI 262
              L +    LQ  DPINIQFTSGTTG PKGATLTH NILNNG+F+GE   LT  DRL I
Sbjct: 176 QDDLVKRQGELQFDDPINIQFTSGTTGNPKGATLTHHNILNNGYFVGESQLLTEKDRLVI 235

Query: 263 PVPLYHCFGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPTMFIAELD 322
           PVPLYHCFGMV+GNL C THG+T++YP +GF+P +VLQ V  E+ T L+GVPTMFIAEL 
Sbjct: 236 PVPLYHCFGMVMGNLGCITHGSTMIYPGEGFEPKSVLQAVHQEKATALYGVPTMFIAELA 295

Query: 323 HPRFAEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSCQSSTDTP 382
            P F  ++LS+LRTGIMAGS CP EVMK+V  +MN++E+ IAYGMTETSPVS Q+S+  P
Sbjct: 296 EPEFETYDLSSLRTGIMAGSICPAEVMKKVNGKMNMKEVQIAYGMTETSPVSTQTSSLDP 355

Query: 383 LSKRVSTVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAIDE 442
             K+V+TVG+ QPHLE KIVDP TG VVP G+ GE CT+GYSVM  YW +E KTREAID 
Sbjct: 356 FEKQVTTVGRTQPHLETKIVDPGTGNVVPRGEIGELCTRGYSVMLKYWNNEEKTREAIDS 415

Query: 443 GGWMHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPD 502
            GWMHTGDLATMD EGYV IVGRIKDMVIRGGENIYP+EIEEFLY HP +++VQV G+PD
Sbjct: 416 AGWMHTGDLATMDEEGYVQIVGRIKDMVIRGGENIYPKEIEEFLYTHPAIEEVQVTGIPD 475

Query: 503 QKYGEELCAWIIAKPGTQP-TEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQKFK 561
            KYGEEL AW+   P   P T +D++AFCKG+IAH+K+P+  +FV  FPMTVTGKIQKFK
Sbjct: 476 DKYGEELIAWVKLAPDAAPVTAEDLQAFCKGKIAHFKIPKNYKFVDEFPMTVTGKIQKFK 535

Query: 562 IRDEMKDQLGLEE 574
           +R+   +++GL++
Sbjct: 536 MREISIEEMGLKK 548


Lambda     K      H
   0.320    0.136    0.412 

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: 869
Number of extensions: 28
Number of successful extensions: 3
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: 578
Length of database: 548
Length adjustment: 36
Effective length of query: 542
Effective length of database: 512
Effective search space:   277504
Effective search space used:   277504
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Sep 17 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