GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hisP in Nostoc punctiforme PCC 73102 ATCC 29133; PCC 73102

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_012411414.1 NPUN_RS25940 ABC transporter ATP-binding protein

Query= TCDB::Q9HU32
         (257 letters)



>NCBI__GCF_000020025.1:WP_012411414.1
          Length = 254

 Score =  142 bits (359), Expect = 5e-39
 Identities = 88/238 (36%), Positives = 129/238 (54%), Gaps = 16/238 (6%)

Query: 8   LEIRNLHKRYG----DLEVLKGISLTARDGDVISILGSSGSGKSTFLRCINLLENPHQGQ 63
           + + N+ K YG    ++  L  ++L    G+  +I+G SGSGKST +  I  L+ P  G 
Sbjct: 22  IRLENIFKIYGSGETEVRALNDVNLIVEQGEYCAIMGPSGSGKSTAMNIIGCLDRPTTGH 81

Query: 64  ILVSGEELRLKKSKNGDLVAADSQQINRLRSE-LGFVFQNFNLWPHMSILDNVIEAPRRV 122
             +           N D+   D + +  +R++ LGFVFQ F+L P ++ L+NVI  P   
Sbjct: 82  YYLD----------NLDVAQMDDRSLAHIRNKKLGFVFQQFHLLPQLTALENVI-LPMLY 130

Query: 123 LGKSKAEAIEIAEGLLAKVGIADKRHSYPAQLSGGQQQRAAIARTLAMQPKVILFDEPTS 182
            G +  E  + A   L +VG+A++ ++ P QLSGGQQQR AIAR +  +P V+L DEPT 
Sbjct: 131 AGVNPKERSDRAIVALTRVGLANRLNNKPTQLSGGQQQRVAIARAIVNRPVVLLADEPTG 190

Query: 183 ALDPEMVQEVLNVIRALAEEGRTMLLVTHEMSFARQVSSEVVFLHQGLVEEQGTPQQV 240
           ALD    QEVL++   L   G T+++VTHE   ARQ    V F    +V    TP  +
Sbjct: 191 ALDSRTTQEVLDIFSELNASGITVVMVTHEPEVARQTQRIVWFRDGQVVHSNLTPSDL 248


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: 142
Number of extensions: 5
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: 254
Length adjustment: 24
Effective length of query: 233
Effective length of database: 230
Effective search space:    53590
Effective search space used:    53590
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 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