Alignments for a candidate for paaZ2 in Marinobacter adhaerens HP15

GapMind for catabolism of small carbon sources

Alignments for a candidate for paaZ2 in Marinobacter adhaerens HP15

Align oxepin-CoA hydrolase (EC 3.3.2.12) (characterized)
to candidate GFF2758 HP15_2702 bifunctional aldehyde dehydrogenase/enoyl-CoA hydratase

Query= BRENDA::P77455
         (681 letters)



>FitnessBrowser__Marino:GFF2758
          Length = 685

 Score =  732 bits (1890), Expect = 0.0
 Identities = 375/681 (55%), Positives = 480/681 (70%), Gaps = 8/681 (1%)

Query: 1   MQQLASFLSGTWQSGRGRSRLIHHAISGEALWEVTSEGLDMAAARQFAIEKGAPALRAMT 60
           M  L SF++G W  G   ++ +  A++GE +     + LD   A ++  + G   L AM 
Sbjct: 5   MSVLKSFIAGQWV-GEKPAKALPSAVNGEIVAHTHDDTLDFKNAVEYGRKVGGKNLMAMD 63

Query: 61  FIERAAMLKAVAKHLLSEKERFYALSAQTGATRADSWVDIEGGIGTLFTYASLGSRELPD 120
           F ERA  LKA+A +L   K+  YALS  TG+T+ D+ +DI+GG GTLF+YAS+G RELP 
Sbjct: 64  FQERALALKAMALYLQEHKKELYALSMHTGSTKGDNGIDIDGGFGTLFSYASMGRRELPS 123

Query: 121 DTLWPEDELIPLSKEGGFAARHLLTSKSGVAVHINAFNFPCWGMLEKLAPTWLGGMPAII 180
             +  E  + PL K   FA  H+L  + GVAVHI+A+NFP WGMLEK APT+L GMP+I+
Sbjct: 124 GNVVHEGPVTPLGKNNHFAGTHILVPRGGVAVHIDAYNFPVWGMLEKFAPTFLAGMPSIV 183

Query: 181 KPATATAQLTQAMVKSIVDSGLVPEGAISLICGSAGDLLDHLDSQDVVTFTGSAATGQML 240
           KPAT+T  +T+  V+ + +SG +PEG++ LI GS GDL DHL+ QDVVTFTGSAAT + L
Sbjct: 184 KPATSTCYVTELAVRLMQESGALPEGSLQLIIGSTGDLFDHLEEQDVVTFTGSAATARKL 243

Query: 241 RVQPNIVAKSIPFTMEADSLNCCVLGEDVTPDQPEFALFIREVVREMTTKAGQKCTAIRR 300
           R  PNI+ +SIPF  EADSLN  +L  DVTP+  EF +F++E+ REMT KAGQKCTAIRR
Sbjct: 244 RNHPNIINRSIPFNAEADSLNSAILAPDVTPEHEEFDVFVKEIRREMTAKAGQKCTAIRR 303

Query: 301 IIVPQALVNAVSDALVARLQKVVVGDPAQEGVKMGALVNAEQRADVQEKVNILLAAGCEI 360
           I VP+  VNAV D L  +L K+ VGDP+ EGV+MGAL + +Q  DV+  +  LL    E+
Sbjct: 304 IFVPKDQVNAVCDKLKEQLSKITVGDPSVEGVRMGALASIDQLEDVKANIQELLKTS-EL 362

Query: 361 RLGGQADLSAAG------AFFPPTLLYCPQPDETPAVHATEAFGPVATLMPAQNQRHALQ 414
            +GG+ +  A G      AF  P LL C  P+     H  EAFGPVAT++P +    A++
Sbjct: 363 VVGGEGNFKATGDGTEKGAFIEPHLLLCRNPENGCGAHDIEAFGPVATVIPYETIDDAVE 422

Query: 415 LACAGGGSLAGTLVTADPQIARQFIADAARTHGRIQILNEESAKESTGHGSPLPQLVHGG 474
           L   G GSL  TL T DP IA +     A  HGR+ +L+ E+AKESTGHGSPLP L HGG
Sbjct: 423 LCSRGRGSLVTTLTTRDPAIAGRIAPLLAAFHGRLHLLDAEAAKESTGHGSPLPMLKHGG 482

Query: 475 PGRAGGGEELGGLRAVKHYMQRTAVQGSPTMLAAISKQWVRGAKVEEDRIHPFRKYFEEL 534
           PGRAGGGEELGG+RAV HY+QRTA+QGSP+MLAA+++++VRGA + E  +HPFR++FE+L
Sbjct: 483 PGRAGGGEELGGIRAVHHYLQRTAIQGSPSMLAAVTREYVRGADLIETDVHPFRRHFEDL 542

Query: 535 QPGDSLLTPRRTMTEADIVNFACLSGDHFYAHMDKIAAAESIFGERVVHGYFVLSAAAGL 594
           Q  +SLLT RRT+TEADIVNF CLSGDHFY H D+IAA +S FG+R+ HGYFVLSAAAGL
Sbjct: 543 QINESLLTHRRTVTEADIVNFGCLSGDHFYMHFDEIAARDSQFGKRIAHGYFVLSAAAGL 602

Query: 595 FVDAGVGPVIANYGLESLRFIEPVKPGDTIQVRLTCKRKTLKKQRSAEEKPTGVVEWAVE 654
           FV  G GPV+ANYGL++LRFIEPV PGDTI+ RLTCKRK  + + S +  P GVV W V+
Sbjct: 603 FVYPGEGPVLANYGLDTLRFIEPVAPGDTIRARLTCKRKIDQGRTSPDGHPQGVVVWDVQ 662

Query: 655 VFNQHQTPVALYSILTLVARQ 675
           V NQ+   VA Y ILTLVA++
Sbjct: 663 VHNQNDEMVASYDILTLVAKK 683


Lambda     K      H
   0.319    0.134    0.395 

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: 1148
Number of extensions: 42
Number of successful extensions: 2
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: 681
Length of database: 685
Length adjustment: 39
Effective length of query: 642
Effective length of database: 646
Effective search space:   414732
Effective search space used:   414732
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: 54 (25.4 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)
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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