GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mtlK in Phaeacidiphilus oryzae TH49

Align ABC transporter for D-mannitol and D-mannose, ATPase component (characterized)
to candidate WP_037572389.1 BS73_RS14235 ABC transporter ATP-binding protein

Query= reanno::pseudo3_N2E3:AO353_25895
         (367 letters)



>NCBI__GCF_000744815.1:WP_037572389.1
          Length = 386

 Score =  240 bits (612), Expect = 5e-68
 Identities = 141/351 (40%), Positives = 204/351 (58%), Gaps = 16/351 (4%)

Query: 4   LKIKNLQKGFEGFSIIKGIDLEVNDREFVVFVGPSGCGKSTLLRLIAGLEEVTAGTIELD 63
           L++  L K F  F+ + G+DL +    F   +G SGCGK+T LR+I+GLE  TAG I L 
Sbjct: 19  LRLTGLTKKFGSFTAVDGVDLTIAQGSFFALLGASGCGKTTTLRMISGLEAPTAGRIHLG 78

Query: 64  GRDITEVSPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVNKAEVEKKVNEAARILEL 123
            +D+T+  P +R +  VFQ YAL+PH+ + +N++F L   G+    V+K V +   ++EL
Sbjct: 79  DQDVTDRKPYRRPVNTVFQNYALFPHLDIFENVAFGLRRRGIRS--VKKPVEDMLDLVEL 136

Query: 124 GPMLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELARLHKEL 183
           G +  RKP QLSGGQ+QR+A+ RA++  P++ L DEPL  LD  LR QM++EL R+  E+
Sbjct: 137 GHLARRKPTQLSGGQQQRIALARALINQPQVLLLDEPLGALDLKLRRQMQIELKRIQLEV 196

Query: 184 QATMIYVTHDQVEAMTLADKVVVLNGGRIEQVGSPLELYHQPANLFVAGFLGTPKMGFLK 243
             T ++VTHDQ EAMT+AD + V+N GRIEQ+GSP ELY  P   FVA FLG  +   + 
Sbjct: 197 GLTFVHVTHDQEEAMTMADTIAVMNHGRIEQLGSPAELYENPNTTFVANFLG--QSNLIA 254

Query: 244 GKVTRVERQNCEVLLDAGTRITLPLSGANLSIGGAVTLGIRPEHLNLA-----LPGDCTL 298
           G V  V     +V    G  + LP +    +  G V LG+RPE + +A     +P     
Sbjct: 255 GTVESVSGDVVQVAAH-GRSLALPAARCR-TTSGPVILGVRPEKVRIAKTEAEVPSGAN- 311

Query: 299 QVTADVSER--LGSDTFCHVLTASGEALTM--RIRGDLASRYGEQLSLHLD 345
            +T  V++   +G  T   V   SGE L +  +  G    R G ++ +H D
Sbjct: 312 HLTGKVTDASFIGVSTQYLVELPSGEELAVFEQNTGQEIQRPGAEVVVHWD 362


Lambda     K      H
   0.321    0.137    0.390 

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: 342
Number of extensions: 20
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: 367
Length of database: 386
Length adjustment: 30
Effective length of query: 337
Effective length of database: 356
Effective search space:   119972
Effective search space used:   119972
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: 50 (23.9 bits)

This GapMind analysis is from Apr 09 2024. 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:

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