GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hisP in Amantichitinum ursilacus IGB-41

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_053938863.1 WG78_RS16125 amino acid ABC transporter ATP-binding protein

Query= TCDB::Q9HU32
         (257 letters)



>NCBI__GCF_001294205.1:WP_053938863.1
          Length = 246

 Score =  244 bits (622), Expect = 2e-69
 Identities = 130/247 (52%), Positives = 171/247 (69%), Gaps = 12/247 (4%)

Query: 8   LEIRNLHKRYG-DLEVLKGISLTARDGDVISILGSSGSGKSTFLRCINLLENPHQGQILV 66
           +    ++K YG D  VLK ISL  + G+V+ + G SGSGKST +R IN LE  + G+I V
Sbjct: 2   IRFNQVNKWYGRDHHVLKNISLEVKQGEVVVVCGPSGSGKSTLIRTINQLEPVNDGEIWV 61

Query: 67  SGEELRLKKSKNGDLVAADSQQINRLRSELGFVFQNFNLWPHMSILDNVIEAPRRVLGKS 126
            G ++   ++            INRLR E+GFVFQ+FNL+PH+S+L N+  AP +V   S
Sbjct: 62  DGVQVNHPRTN-----------INRLREEVGFVFQHFNLYPHLSVLQNITLAPVKVRKMS 110

Query: 127 KAEAIEIAEGLLAKVGIADKRHSYPAQLSGGQQQRAAIARTLAMQPKVILFDEPTSALDP 186
           +A+A +    LL +VG+++KR +YP+QLSGGQQQR AIAR LAMQPKV+LFDEPTSALDP
Sbjct: 111 QADADQRGMELLERVGLSNKRDAYPSQLSGGQQQRVAIARGLAMQPKVMLFDEPTSALDP 170

Query: 187 EMVQEVLNVIRALAEEGRTMLLVTHEMSFARQVSSEVVFLHQGLVEEQGTPQQVFENPQS 246
           EM+ EVL V++ LAE G TM++VTHEM FAR+V+  VVFL  G + EQ  P Q F NPQ 
Sbjct: 171 EMIGEVLKVMQNLAESGMTMMVVTHEMGFAREVADRVVFLDHGEILEQAAPAQFFNNPQC 230

Query: 247 ARCKQFM 253
            R +QF+
Sbjct: 231 DRAQQFL 237


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: 178
Number of extensions: 3
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: 246
Length adjustment: 24
Effective length of query: 233
Effective length of database: 222
Effective search space:    51726
Effective search space used:    51726
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: 46 (22.3 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