GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aatP in Collimonas arenae Ter10

Align ABC transporter for L-Asparagine and possibly other L-amino acids, putative ATPase component (characterized)
to candidate WP_156477079.1 CAter10_RS07860 amino acid ABC transporter ATP-binding protein

Query= reanno::pseudo13_GW456_L13:PfGW456L13_4773
         (244 letters)



>NCBI__GCF_001584165.1:WP_156477079.1
          Length = 255

 Score =  230 bits (586), Expect = 2e-65
 Identities = 133/248 (53%), Positives = 167/248 (67%), Gaps = 10/248 (4%)

Query: 1   MISIKSINKWYGDFQVLTDCSTEVKKGEVIVVCGPSGSGKSTLIKCVNALEPFQKGDIVV 60
           MISI+++ K +GD  VL D S E+ KG V+ + GPSGSGKSTL++C+N L     G + V
Sbjct: 1   MISIRNLKKCFGDNVVLKDISLEISKGSVVAMIGPSGSGKSTLLRCINLLTIPDAGTVNV 60

Query: 61  DGTSIA-DPK-TNLPK------LRSRVGMVFQHFELFPHLTITENLTIAQIKVLGRSKEE 112
            G SIA D K T LPK       RS+ GMVFQHF LFPH+T+ +N+    + VL   K++
Sbjct: 61  GGQSIAFDGKHTKLPKAKDLAHFRSKTGMVFQHFNLFPHMTVRQNVMEGMVTVLKIPKQD 120

Query: 113 ATKKGLQLLERVGLSAHAHKHPGQLSGGQQQRVAIARALAMDPIVMLFDEPTSALDPEMV 172
           A      LL+RVGLS  A  +PG LSGGQ+QRVAIARALAM P VMLFDE TSALDPE+V
Sbjct: 121 ARITADALLQRVGLSDRADAYPGMLSGGQKQRVAIARALAMKPDVMLFDEATSALDPELV 180

Query: 173 NEVLDVMVQLAHEGMTMMCVTHEMGFARKVADRVIFMDQGKIIEDCKKEEFFGDINARAE 232
            EVL V+  LA +GMTM+ VTHE+ FAR+VAD+VIFM  G ++E C       D N   E
Sbjct: 181 GEVLSVIRSLAADGMTMILVTHEIAFAREVADQVIFMRDGVVVE-CGPPSVVID-NPEKE 238

Query: 233 RTQHFLNK 240
            T+ FL++
Sbjct: 239 ATRSFLSR 246


Lambda     K      H
   0.321    0.136    0.394 

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: 192
Number of extensions: 10
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: 244
Length of database: 255
Length adjustment: 24
Effective length of query: 220
Effective length of database: 231
Effective search space:    50820
Effective search space used:    50820
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 (21.9 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