GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_2560 in Thiothrix lacustris DSM 21227

Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate WP_028488909.1 Q394_RS0108480 spermidine/putrescine ABC transporter ATP-binding protein PotA

Query= reanno::acidovorax_3H11:Ac3H11_2560
         (259 letters)



>NCBI__GCF_000621325.1:WP_028488909.1
          Length = 369

 Score =  147 bits (372), Expect = 2e-40
 Identities = 83/190 (43%), Positives = 115/190 (60%), Gaps = 3/190 (1%)

Query: 22  QALQPVDFEVRDNDFVTILGPSGCGKSTLLRIVAGLDHATSGRVLLDGAPVEGPGAER-- 79
           + L   +  ++D +F TILGPSGCGK+T+LR++AG +    G++LL+G  +    AE+  
Sbjct: 20  EVLSDFNLTIQDGEFFTILGPSGCGKTTVLRLIAGFEQPNEGQILLNGDDIARIPAEKRP 79

Query: 80  -GMVFQSYTLFPWLTIEQNIRFGLRERGMPEAQQKERAAYFIAKVGLRGFEQHFPKQLSG 138
              VFQSY LFP LT+  N+ FGL+  G+       R A  +A V L  F    P QLSG
Sbjct: 80  FNTVFQSYALFPHLTVFDNVAFGLKMAGVDVQDIAVRVADALAIVRLSEFATRKPHQLSG 139

Query: 139 GMQQRTAIARALANDPKILLMDEPFGALDNQTRVLMQELLLGIWEAERKTVLFVTHDIDE 198
           G +QR AIARA+ N PKILL+DE   ALD + R  MQ  L  +      T ++VTHD +E
Sbjct: 140 GQKQRVAIARAVVNRPKILLLDESLSALDYKLRQQMQLELKQLQRQLGITFVYVTHDQEE 199

Query: 199 AIFMANRVAV 208
           A+ M++R+ V
Sbjct: 200 ALSMSDRILV 209


Lambda     K      H
   0.322    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: 227
Number of extensions: 11
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: 259
Length of database: 369
Length adjustment: 27
Effective length of query: 232
Effective length of database: 342
Effective search space:    79344
Effective search space used:    79344
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: 48 (23.1 bits)

This GapMind analysis is from Apr 09 2024. 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