GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aatP in Skermanella stibiiresistens SB22

Align ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized)
to candidate WP_037453109.1 N825_RS14315 ATP-binding cassette domain-containing protein

Query= reanno::pseudo1_N1B4:Pf1N1B4_774
         (244 letters)



>NCBI__GCF_000576635.1:WP_037453109.1
          Length = 250

 Score =  229 bits (584), Expect = 4e-65
 Identities = 126/252 (50%), Positives = 166/252 (65%), Gaps = 12/252 (4%)

Query: 1   MISIKNVNKWYGDFQVLTDCSTEVKKGEVIVVCGPSGSGKSTLIKCVNALEPFQKGDVIV 60
           M+    V K +G  +VL+     +   EV+ + GPSGSGKSTL++C+N LE    G ++V
Sbjct: 1   MVEAIGVRKSFGAVEVLSGIDMTILPREVVCLLGPSGSGKSTLLRCINHLEKLSGGRILV 60

Query: 61  DGTSIADPK----------TNLPKLRSRVGMVFQHFELFPHLSIMDNLTIAQVKVLGRSK 110
           DG  I   +            L + R  +GMVFQ F LFPHL ++ N+T A + + G S+
Sbjct: 61  DGELIGYRERGDRLHELGSAELARQRRDIGMVFQRFNLFPHLDVVGNITQAPMLIKGESR 120

Query: 111 EEASKKALQLLERVGLSAHAKKHPGQLSGGQQQRVAIARALAMDPIVMLFDEPTSALDPE 170
            EA+++A +LLE V L+  A  +P QLSGGQQQRVAIARALAM P +MLFDEPTSALDPE
Sbjct: 121 AEATRRAHELLEIVDLAGKANAYPHQLSGGQQQRVAIARALAMRPKLMLFDEPTSALDPE 180

Query: 171 MVNEVLDVMVQLAHEGMTMMCVTHEMGFARKVADRVIFMDQGKIIEDCKKEEFFGDITAR 230
           +V EVL VM +LA EGMTM+ VTHEMGFAR+VADRVIFMD+G ++E     +       R
Sbjct: 181 LVGEVLAVMKRLALEGMTMLVVTHEMGFAREVADRVIFMDRGVVVEQGTAADVIA--RPR 238

Query: 231 SDRAQHFLEKIL 242
            DR + FL+++L
Sbjct: 239 HDRTKAFLKRVL 250


Lambda     K      H
   0.321    0.135    0.390 

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: 196
Number of extensions: 9
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: 250
Length adjustment: 24
Effective length of query: 220
Effective length of database: 226
Effective search space:    49720
Effective search space used:    49720
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