GapMind for catabolism of small carbon sources

 

Aligments for a candidate for Ac3H11_2560 in Echinicola vietnamensis KMM 6221, DSM 17526

Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate Echvi_1096 Echvi_1096 nitrate transport ATP-binding subunits C and D

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



>lcl|FitnessBrowser__Cola:Echvi_1096 Echvi_1096 nitrate transport
           ATP-binding subunits C and D
          Length = 294

 Score =  181 bits (458), Expect = 2e-50
 Identities = 96/252 (38%), Positives = 152/252 (60%), Gaps = 7/252 (2%)

Query: 1   MSSVSIQAVSRVFETAKGQRTQALQPVDFEVRDNDFVTILGPSGCGKSTLLRIVAGLDHA 60
           M+ + +  VS+ F      R   L  ++ +V + +FV I+G SG GK+TL+ ++ GL   
Sbjct: 1   MAIIELNNVSKSFGMG-ASRVDVLSDINLQVAEGEFVAIVGFSGSGKTTLINLLNGLAFP 59

Query: 61  TSGRVLLDGAPVEGPGAERGMVFQSYTLFPWLTIEQNIRFGLRERGMPEAQQKERAAY-- 118
             G VLL G PV GPG +RG++FQ+Y+L PWL++  N++  + E   P+   KE+A++  
Sbjct: 60  DQGEVLLHGQPVTGPGPDRGVIFQNYSLLPWLSVYNNVKLAVDEV-FPQLSSKEKASHIK 118

Query: 119 -FIAKVGLRGFEQHFPKQLSGGMQQRTAIARALANDPKILLMDEPFGALDNQTRVLMQEL 177
            +I  V L       PK+LSGGM+QR ++ARALA +P+ILLMDEP  ALD  TR  +QE 
Sbjct: 119 KYIGMVNLTPAMDKLPKELSGGMRQRVSVARALAMNPEILLMDEPLSALDALTRGSLQEE 178

Query: 178 LLGIWEAERKTVLFVTHDIDEAIFMANRVAVFSARP-GRIKTELAVDLPHPRHYT-IKTS 235
           ++ IW  ++KT + +T+D+DE I MA+R+   +  P   +  E  +D+  PR  + I  +
Sbjct: 179 IIRIWSQDKKTAILITNDVDEGILMADRIIPLTPGPKATLGPEFTIDIERPRDLSAINQN 238

Query: 236 PEFMDLKARLTE 247
            ++  L+  + E
Sbjct: 239 DDYKKLRNEIIE 250


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: 199
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: 294
Length adjustment: 25
Effective length of query: 234
Effective length of database: 269
Effective search space:    62946
Effective search space used:    62946
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: 47 (22.7 bits)

This GapMind analysis is from Sep 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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