GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aatP in Erythrobacter marinus HWDM-33

Align Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized)
to candidate WP_047092042.1 AAV99_RS00435 ABC transporter ATP-binding protein

Query= TCDB::P0AAG3
         (241 letters)



>NCBI__GCF_001013305.1:WP_047092042.1
          Length = 233

 Score =  127 bits (319), Expect = 2e-34
 Identities = 79/208 (37%), Positives = 120/208 (57%), Gaps = 9/208 (4%)

Query: 15  QVLTDCSTEVKKGEVVVVCGPSGSGKSTLIKTVNGLEPVQQGEITVDG---IVVNDKKTD 71
           ++L     +V +GE + + GPSGSGKS+L+  ++GLE    G++TV G     +N+    
Sbjct: 28  EILRGIDLDVARGETLALLGPSGSGKSSLMSVLSGLERATSGKLTVAGEDFTALNEDALA 87

Query: 72  LAKLRSRVGMVFQHFELFPHLSIIENLTLAQVKVLKRDKAPAREKALKLLERVGLSAHAN 131
           +A+ R R+G+V Q F L P ++ +EN+    +++   D A   E+A   LE VGL     
Sbjct: 88  MAR-RGRIGIVLQAFHLLPTMTAVENVA-TPLELAGEDGA--WERATAELEAVGLGHRLT 143

Query: 132 KFPAQLSGGQQQRVAIARALCMDPIAMLFDEPTSALDPEMINEVLDVMVE-LANEGMTMM 190
            +PAQLSGG+QQRVAIARA+   P  +  DEPT  LD      V D + E  A  G T++
Sbjct: 144 HYPAQLSGGEQQRVAIARAIVSRPPLIFADEPTGNLDTNTGASVEDALFERRAETGATLI 203

Query: 191 VVTHEMGFARKVANRVIFMDEGKIVEDS 218
           ++TH+   A +  NRV+ + +G I  D+
Sbjct: 204 IITHDRKLAER-CNRVVTLGDGLIATDT 230


Lambda     K      H
   0.320    0.135    0.383 

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: 116
Number of extensions: 4
Number of successful extensions: 3
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: 241
Length of database: 233
Length adjustment: 23
Effective length of query: 218
Effective length of database: 210
Effective search space:    45780
Effective search space used:    45780
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 (21.8 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