GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hisP in Marinobacter adhaerens HP15

Align Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale)
to candidate GFF2243 HP15_2193 amino-acid ABC transporter ATP-binding protein-like protein

Query= uniprot:Q88GX0
         (260 letters)



>FitnessBrowser__Marino:GFF2243
          Length = 256

 Score =  336 bits (862), Expect = 2e-97
 Identities = 161/247 (65%), Positives = 199/247 (80%)

Query: 13  EPDPRPVLIRIEGLNKHYGAFHVLRDIDLQVREGERIVLCGPSGSGKSTLIRCINRLEVA 72
           +P  +P +IR+EG++K YG FHVL+D++L V +GERIV+CGPSGSGKST IRCINRLE  
Sbjct: 8   QPGKKPGIIRVEGMHKWYGDFHVLKDLNLTVDQGERIVICGPSGSGKSTFIRCINRLEEH 67

Query: 73  QQGSIQVDGIDLAATTREAAQVRSDIGMVFQHFNLFPHMSVLDNCLLAPTSVRGLSRKDA 132
           QQG I VDGI+L    R    VR ++GMVFQHFNLFPH++VL+NC L+P  VR   RK+A
Sbjct: 68  QQGKIIVDGIELTDDVRHIDTVRREVGMVFQHFNLFPHLTVLENCCLSPIWVRKTPRKEA 127

Query: 133 EERARMYLSKVGIESQAHKYPSQLSGGQQQRVAIARALCMKPRIMLFDEPTSALDPEMVA 192
           E  A  YL +V I  QA+K+P QLSGGQQQRVAIARALCMKP+IMLFDEPTSALDPEM+ 
Sbjct: 128 EASAMEYLERVKIPDQANKFPGQLSGGQQQRVAIARALCMKPKIMLFDEPTSALDPEMIK 187

Query: 193 EVLDVLVQLAGTGMTMLCVTHEMGFARQVAERVLFLEGGQIIEDSPPQVFFNQPRTERAK 252
           EVLDV+++LAG+GMTMLCVTHEMGFA+ VA+RV+F++GG+I+E +PP  FF  P+  R +
Sbjct: 188 EVLDVMIELAGSGMTMLCVTHEMGFAKTVADRVIFMDGGEIVEQAPPHEFFTNPQEARTQ 247

Query: 253 AFLAQIL 259
            FL QIL
Sbjct: 248 KFLQQIL 254


Lambda     K      H
   0.322    0.137    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: 233
Number of extensions: 4
Number of successful extensions: 1
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: 260
Length of database: 256
Length adjustment: 24
Effective length of query: 236
Effective length of database: 232
Effective search space:    54752
Effective search space used:    54752
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 (21.9 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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 paper from 2022 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