Alignments for a candidate for paaK in Marinobacter adhaerens HP15

GapMind for catabolism of small carbon sources

Alignments for a candidate for paaK in Marinobacter adhaerens HP15

Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate GFF3986 HP15_3926 acyl-CoA synthetase

Query= BRENDA::A7KUK6
         (562 letters)



>FitnessBrowser__Marino:GFF3986
          Length = 554

 Score =  182 bits (461), Expect = 4e-50
 Identities = 161/562 (28%), Positives = 263/562 (46%), Gaps = 55/562 (9%)

Query: 12  IPEVDLWTFLFERKDRAYPDDK-IIYQDADTQRHYTYKSLRDASLDFGKGLKALYEWRKG 70
           +P+  ++T L E   R YPD   II+ DA      TY+ L +  ++   G       +KG
Sbjct: 19  LPKTSVYTNL-EISARRYPDHTAIIFYDAPI----TYRRLNE-EVETLAGYLQEQGVKKG 72

Query: 71  DVLALFTPNSIDTPVVMWGTLWAGGTISPANPGYTVDELAFQLKNSHAK----GLVTQAS 126
           D + L+  NS    +  +  L A   + P NP     EL   + ++ A     G      
Sbjct: 73  DRVLLYMQNSPQYVISYYAILRADAVVIPVNPMNRSAELEHFIADTGATVCLAGQELAGF 132

Query: 127 VLPVAREAAKKVGMPEDRIILIGDQRDPDARVKHFTSV--RNISGATRYR---------- 174
           + P+  ++     +       I  + D D   +    V  R++ G   +           
Sbjct: 133 IAPMIGDSNLDQVVVASYSTYIDPETDLDLPAEVAAPVWSRDLPGVVTWEVAMAAGYAPG 192

Query: 175 KQKITPAKDVAFLVYSSGTTGVPKGVMISHRNIVANIRQQFIAEGEMLSWN-GGPDGKGD 233
               TP  D+A + YSSGTTG PKG M +HR+++A    +         WN   PD    
Sbjct: 193 PHTATP-DDLAVIPYSSGTTGAPKGCMHTHRSVMATAIHRIF-------WNLTTPDSVQ- 243

Query: 234 RVLAFLPFYHIYGLTCLITQALYKGYHLIVMSKFDIEKWCAHVQNYRCS-FSYIVPPVVL 292
             LA LPF+H+ G+T  +   +  G   ++M+++D       ++ Y+ + ++ IV   V 
Sbjct: 244 --LATLPFFHVTGMTGSMNGPIAAGAASVIMTRWDRTTASRLIERYKVTGWTNIVTMAVD 301

Query: 293 LLGKHPVVDKYDLSSLRMMNSGAAPLTQELVEAVYSRIKVGIKQGYGLSETSPTTH-SQR 351
            L  +P + +YDLSSL M+  G A +   + E +     +   +GYGLSET   TH +  
Sbjct: 302 FLS-NPDIGQYDLSSLNMIGGGGATMPSAVAEKLKRMTGLDYIEGYGLSETMAATHINPN 360

Query: 352 WEDWREAMGSVGRLMPNMQAKYMTMPEDGSEPKEVGEGEVGELYLKGPNVFLGYHENPEA 411
                + +G     +P        +  D  E K  G GE GE+   GP V  GY   P  
Sbjct: 361 AHPKSQCLG-----IPVFDVDSRIIDVDTLEEK--GPGETGEIVSCGPQVTRGYWNRPSE 413

Query: 412 TKGCLSE-DG--WFQTGDVGYQDAKGNFYITDRVKELIKYKGFQVPPAELEGYLVDNDAI 468
           T+    E DG  +F+TGD+GY D  G F++ DRVK +I   G++V P+E+EG +  + AI
Sbjct: 414 TEAAFVEIDGKQFFRTGDLGYYDEDGYFFMVDRVKRMINASGYKVWPSEVEGMMYRHPAI 473

Query: 469 DDVAVIGIESETHGSEVPMACVVRSAKSKSSGTSEKDEAARIIKWLDSKVASHKRLRGGV 528
            +V +I       G E   AC+V + +++      +  A  II W   ++A++K +   +
Sbjct: 474 HEVCIISAPDPKRG-ETVKACIVLTPEAEG-----QTSAGDIIAWCKEQMATYK-VPTMI 526

Query: 529 HFVDEIPKNPSGKILRRILKQK 550
            FVD++PK+P+GK++ R L+++
Sbjct: 527 DFVDQLPKSPTGKLMWRALQEE 548


Lambda     K      H
   0.317    0.136    0.410 

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: 814
Number of extensions: 40
Number of successful extensions: 7
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: 562
Length of database: 554
Length adjustment: 36
Effective length of query: 526
Effective length of database: 518
Effective search space:   272468
Effective search space used:   272468
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: 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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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