GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aatP in Sulfurimonas denitrificans DSM 1251

Align PP1068, component of Acidic amino acid uptake porter, AatJMQP (characterized)
to candidate WP_011372556.1 SUDEN_RS04860 sulfate/molybdate ABC transporter ATP-binding protein

Query= TCDB::Q88NY5
         (256 letters)



>NCBI__GCF_000012965.1:WP_011372556.1
          Length = 290

 Score =  124 bits (311), Expect = 2e-33
 Identities = 79/228 (34%), Positives = 128/228 (56%), Gaps = 11/228 (4%)

Query: 16  IKNVNKWYGDFQVLTDCSTEVKKGEVVVVCGPSGSGKSTLIKCVNALEPFQKGDIVVDGT 75
           IK +N   G+  +  D   +++ GE + + G SGSGK+TL++ +  LE  + G I VD  
Sbjct: 7   IKPLNTADGEINLAVD--KKIEDGEFLTLFGKSGSGKTTLLRIIAGLEVPESGYIKVDNE 64

Query: 76  SIADPKT--NLPKLRSRVGMVFQHFELFPHLTITENLTIAQRKVLGRSEAEATKKGLALL 133
              D K   N+P  R  VG VFQ + LFP++++ +NL  A +      +    KK   +L
Sbjct: 65  VWFDSKRGINIPPQRRNVGFVFQDYALFPNMSVEDNLKFALQ------DKNKFKKVDDIL 118

Query: 134 DRVGLSAHAKKHPGQLSGGQQQRVAIARALAMDPIVMLFDEPTSALDPEMVSEVLDVMVQ 193
             + +   +K  P  LSGGQ+QRVA+ARAL  +P ++L DEP SALD  M  ++ D +  
Sbjct: 119 KIMEIQNLSKMKPQHLSGGQKQRVAVARALMREPKILLLDEPLSALDSTMRQKLQDELFF 178

Query: 194 LAQE-GMTMMCVTHEMGFARKVANRVIFMDKGSIIEDCTKEEFFGDQS 240
           + Q+ G+  + V+H++G   ++++RV  +  G I  D +  E F +Q+
Sbjct: 179 IHQKFGIISLLVSHDIGEIFRLSSRVFKISSGEITHDGSPSEVFANQN 226


Lambda     K      H
   0.319    0.134    0.383 

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: 149
Number of extensions: 9
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: 256
Length of database: 290
Length adjustment: 25
Effective length of query: 231
Effective length of database: 265
Effective search space:    61215
Effective search space used:    61215
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: 47 (22.7 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