GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hisP in Azospirillum thiophilum BV-S

Align Probable ATP-binding component of ABC transporter, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized)
to candidate WP_045582841.1 AL072_RS18480 amino acid ABC transporter ATP-binding protein

Query= TCDB::Q9HU32
         (257 letters)



>NCBI__GCF_001305595.1:WP_045582841.1
          Length = 251

 Score =  242 bits (618), Expect = 5e-69
 Identities = 129/251 (51%), Positives = 170/251 (67%), Gaps = 9/251 (3%)

Query: 3   EATPALEIRNLHKRYGDLEVLKGISLTARDGDVISILGSSGSGKSTFLRCINLLENPHQG 62
           ++ P +E+R+++K +G   VLKG++L+ RDG V+ I+G SGSGKST LRCIN L    +G
Sbjct: 6   QSAPFIEMRDVYKSFGSTAVLKGVTLSVRDGGVVCIIGPSGSGKSTILRCINGLMTIDRG 65

Query: 63  QILVSGEELRLKKSKNGDLVAADSQQINRLRSELGFVFQNFNLWPHMSILDNVIEAPRRV 122
            I V    +   KS          +Q+  LR ++  VFQ +NL+PH ++L N+  AP +V
Sbjct: 66  TIRVGSFAVETLKS---------DKQLVPLRHQVAMVFQQYNLFPHRTVLQNLTMAPVQV 116

Query: 123 LGKSKAEAIEIAEGLLAKVGIADKRHSYPAQLSGGQQQRAAIARTLAMQPKVILFDEPTS 182
           LG++ A   E A  LLAKV +  K+ SYP +LSGGQQQR AIAR LAMQPKVILFDE T+
Sbjct: 117 LGENPAAVRERALALLAKVRLTGKQDSYPGELSGGQQQRVAIARALAMQPKVILFDEVTA 176

Query: 183 ALDPEMVQEVLNVIRALAEEGRTMLLVTHEMSFARQVSSEVVFLHQGLVEEQGTPQQVFE 242
           ALDPEMV EVLNVIR LA EG T +LVTHEM FA++V+ EV F  +G++ E G P  +F+
Sbjct: 177 ALDPEMVSEVLNVIRDLAREGMTCVLVTHEMRFAQEVADEVFFTDRGVIVEHGPPGTIFQ 236

Query: 243 NPQSARCKQFM 253
           NP   R K F+
Sbjct: 237 NPTDPRLKAFL 247


Lambda     K      H
   0.317    0.133    0.367 

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: 165
Number of extensions: 7
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: 257
Length of database: 251
Length adjustment: 24
Effective length of query: 233
Effective length of database: 227
Effective search space:    52891
Effective search space used:    52891
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 (21.7 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Sep 24 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:

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