GapMind for catabolism of small carbon sources

 

Aligments for a candidate for pimB in Marinobacter adhaerens HP15

Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate GFF49 HP15_49 acetyl-CoA acetyltransferase

Query= metacyc::MONOMER-20679
         (395 letters)



>lcl|FitnessBrowser__Marino:GFF49 HP15_49 acetyl-CoA
           acetyltransferase
          Length = 391

 Score =  254 bits (650), Expect = 2e-72
 Identities = 155/395 (39%), Positives = 217/395 (54%), Gaps = 10/395 (2%)

Query: 1   MTEAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRAGIDPKEVEDVVMGAAMQQ 60
           M + VIV   RTP+G+ +RG+L       L    +   + R G+  + ++DVV G   Q 
Sbjct: 1   MKDVVIVDAVRTPVGR-FRGSLAGVRADHLGALVLNELLYRNGLAAESIDDVVFGCVTQI 59

Query: 61  GATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESI 120
           G    NIAR +LL AG P +  G TIDR+C SG  A+  A  ++     EI V GG E++
Sbjct: 60  GEQSANIARTSLLGAGWPTSVPGLTIDRKCGSGEAAVHCAFGAIAAGSAEIVVAGGAENM 119

Query: 121 SLVQNDKMNTFHAVDPALEAIKGDVY--MAMLDTAETVAKRYGISRERQDEYSLESQRRT 178
           S V        H    A   +  D Y   +  + AE VA+++ + RE+ D ++LES RR 
Sbjct: 120 SRVPMGSNRDLHG--EAFGHLVSDRYEMTSQGEAAERVAEKWNLDREQLDAFALESHRRA 177

Query: 179 AAAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEGLAGLK-AVR 237
           A A   G F  EI P+     V D         +   + DE  R +T+ E LA LK + R
Sbjct: 178 AVAADSGYFKSEIVPVP----VADYRENGAEKVEGKFAADETIRRDTSLEKLATLKTSFR 233

Query: 238 GEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEPDEMGIGPVFA 297
            E   ITAGN+SQ+SDG SA ++MS   A   GLKP    R + + G +P  M  GP+ A
Sbjct: 234 KENGRITAGNSSQISDGCSALLLMSSDVARNLGLKPKARIRAVTTVGADPTLMLTGPIGA 293

Query: 298 VPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLNVNGGAISVGHPYGMSGA 357
             ++L + GL +D+I L+E+NEAFA   L    ++G DPE+LNVNGGAI++GHP G SGA
Sbjct: 294 TRKVLAKAGLELDEIDLFEINEAFASVPLAWMKEVGADPERLNVNGGAIALGHPLGASGA 353

Query: 358 RLAGHALIEGRRRKAKYAVVTMCVGGGMGSAGLFE 392
           R+    L E  RR+ +YA+  +C  GGMG+A + E
Sbjct: 354 RIMTSMLNELERRRGRYALQAICCAGGMGTATIIE 388


Lambda     K      H
   0.316    0.134    0.378 

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: 385
Number of extensions: 16
Number of successful extensions: 4
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: 395
Length of database: 391
Length adjustment: 31
Effective length of query: 364
Effective length of database: 360
Effective search space:   131040
Effective search space used:   131040
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 (21.6 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 17 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:

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:

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:

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 preprint on GapMind for carbon sources, or view the source code.

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