GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_2560 in Shewanella sp. ANA-3

Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate 7026118 Shewana3_3260 ABC transporter related (RefSeq)

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



>FitnessBrowser__ANA3:7026118
          Length = 246

 Score =  131 bits (330), Expect = 1e-35
 Identities = 80/201 (39%), Positives = 110/201 (54%), Gaps = 11/201 (5%)

Query: 4   VSIQAVSRVFETAKGQRTQALQPVDFEVRDNDFVTILGPSGCGKSTLLRIVAGLDHATSG 63
           +S++ +S+VF+T   + T AL+  + EV + +FV + GPSG GK+T L I   L+  T G
Sbjct: 2   LSMKNISKVFKTDLVE-THALRDFNLEVNEGEFVAVTGPSGSGKTTFLNIAGLLEGFTHG 60

Query: 64  RVLLDGAPVEGPGAER---------GMVFQSYTLFPWLTIEQNIRFGLRERGMPEAQQKE 114
              LDG  V      +         G +FQ + L P L + +NI   LR RG    ++K 
Sbjct: 61  DYFLDGINVSNLSDNKSAAVRNEKIGFIFQGFNLIPDLNLAENIEVPLRYRGFSAKERKR 120

Query: 115 RAAYFIAKVGLRGFEQHFPKQLSGGMQQRTAIARALANDPKILLMDEPFGALDNQTRVLM 174
           R    + +VGL    +H P QLSGG QQR AIARALA +P+ LL DEP G LD+     +
Sbjct: 121 RVEQALEQVGLGARMKHLPTQLSGGQQQRVAIARALAGEPRFLLADEPTGNLDSLMARQV 180

Query: 175 QELLLGIWEAERKTVLFVTHD 195
            ELL  I      T++ VTHD
Sbjct: 181 MELLENI-NQSGTTIIMVTHD 200


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: 146
Number of extensions: 7
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: 246
Length adjustment: 24
Effective length of query: 235
Effective length of database: 222
Effective search space:    52170
Effective search space used:    52170
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 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:

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