GapMind for catabolism of small carbon sources

 

Alignments for a candidate for exuT in Caulobacter crescentus NA1000

Align Hexuronate transporter (characterized)
to candidate CCNA_01576 CCNA_01576 major facilitator superfamily transporter

Query= SwissProt::P0AA78
         (432 letters)



>FitnessBrowser__Caulo:CCNA_01576
          Length = 431

 Score =  231 bits (590), Expect = 3e-65
 Identities = 136/408 (33%), Positives = 217/408 (53%), Gaps = 9/408 (2%)

Query: 3   KIKGLRWYMIALVTLGTVLGYLTRNTVAAAAPTLMEELNISTQQYSYIIAAYSAAYTVMQ 62
           KI   RW ++ L+ L  V+ Y+ R T+      L  E   S   Y+ ++  +  +Y V  
Sbjct: 19  KIGRYRWIIVTLLFLAMVINYVDRQTIGFLKHDLSVEFGWSEHDYANLVFYFQLSYAVAY 78

Query: 63  PVAGYVLDVLGTKIGYAMFAVLWAVFCGATALAGSWGGLAVARGAVGAAEAAMIPAGLKA 122
            V G V+D +G + G+ +  ++W V   A A A    G   AR A+G  EA   P G+KA
Sbjct: 79  LVWGKVMDKIGARWGFGIAFLIWQVAHIAHAGARGLTGFIFARMALGVGEAGGFPGGIKA 138

Query: 123 SSEWFPAKERSIAVGYFNVGSSIGAMIAPPLVVWAIVMHSWQMAFIISGALSFIWAMAWL 182
            +EWFP KER+ A G FN G++IGA++ P +V   ++   WQMAFI++G    IW   WL
Sbjct: 139 VTEWFPKKERAFATGIFNAGTNIGAIVTPLVVPAIVLAWGWQMAFIVTGVAGLIWLPIWL 198

Query: 183 IFYKHPRDQKHLTDEERDYIINGQEAQHQVSTAKKMSVGQILRNRQFWGIALPRFLAEPA 242
           + Y+ PR+ K+L+  E  +I      Q      +K++  ++L  R+ W  A+ +FL +P 
Sbjct: 199 LVYRTPRETKNLSAAELAHI-----EQDPADPVEKIAWTKLLTKRETWAYAIGKFLIDPI 253

Query: 243 WGTFNAWIPLFMFKVYGFNLKEIAMFAWMPMLFADLGCILGGYLPPLFQRWFGVNLIVSR 302
           W  F  W+P F+ K YG +LK          L +D G + GG+L   F +  G ++  +R
Sbjct: 254 WWMFLFWLPDFLGKRYGLDLKTFGPPIVAIYLLSDAGSVGGGWLSSNFMK-MGWSINRAR 312

Query: 303 KMVVTLGAVLMIGPGMIGLFTNP-YVAIMLLCIGGFAHQALSGALITLSSDVFGRNEVAT 361
           K+ + + A+L + P M   F +  +VA++++ +   AHQ  S  L TL SDVF R  V +
Sbjct: 313 KITMLICALLAV-PVMFASFADSLWVAVLIIGVATAAHQGFSANLYTLPSDVFPRGAVGS 371

Query: 362 ANGLTGMSAWLASTLFALVVGALADTIG-FSPLFAVLAVFDLLGALVI 408
             G+ GM   +   +F+  +G + ++IG ++P+F V     LL  LV+
Sbjct: 372 VVGIGGMLGAVGGMVFSKYIGGVLESIGTYTPIFIVAGSAYLLALLVV 419


Lambda     K      H
   0.326    0.138    0.437 

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: 635
Number of extensions: 46
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 432
Length of database: 431
Length adjustment: 32
Effective length of query: 400
Effective length of database: 399
Effective search space:   159600
Effective search space used:   159600
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 51 (24.3 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