GapMind for catabolism of small carbon sources

 

Alignments for a candidate for artP in Flavobacterium beibuense F44-8

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_035130886.1 Q763_RS02520 ABC transporter ATP-binding protein

Query= TCDB::Q9HU32
         (257 letters)



>NCBI__GCF_000769915.1:WP_035130886.1
          Length = 222

 Score =  136 bits (342), Expect = 4e-37
 Identities = 79/222 (35%), Positives = 129/222 (58%), Gaps = 16/222 (7%)

Query: 8   LEIRNLHKRYGDLEVLKGISLTARDGDVISILGSSGSGKSTFLRCINLLENPHQGQ---I 64
           ++ +N+HK Y  L VLKG+ L  + G+V+SI+G+SG+GK+T L+ +  L+ P   +   +
Sbjct: 2   IQAKNIHKYYDSLHVLKGVDLHIKKGEVVSIVGASGAGKTTLLQILGTLDKPKSEKGTSL 61

Query: 65  LVSGEELRLKKSKNGDLVAADSQQINRLRS-ELGFVFQNFNLWPHMSILDNVIEAPRRVL 123
           L+ GE++   K K           +++ R+ +LGF+FQ   L+P  + L+NV   P  + 
Sbjct: 62  LIDGEDVLNMKDK----------ALSKFRNLKLGFIFQFHQLFPEFTALENVC-IPAFIA 110

Query: 124 GKSKAEAIEIAEGLLAKVGIADKRHSYPAQLSGGQQQRAAIARTLAMQPKVILFDEPTSA 183
           GK KAE    A+ LL  +G++ + +  P +LSGG+QQR A+AR L  +P VI  DEP+  
Sbjct: 111 GKQKAETEAEAKKLLEYLGLSHRINHKPGELSGGEQQRVAVARALINKPAVIFADEPSGN 170

Query: 184 LDPEMVQEVLNVIRALAEE-GRTMLLVTHEMSFARQVSSEVV 224
           LD    + + N+   L +E G+T ++VTH    A     ++V
Sbjct: 171 LDTHSAENLHNLFFKLRDEMGQTFVIVTHNEELANMADRKLV 212


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: 135
Number of extensions: 9
Number of successful extensions: 4
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: 222
Length adjustment: 23
Effective length of query: 234
Effective length of database: 199
Effective search space:    46566
Effective search space used:    46566
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