GapMind for catabolism of small carbon sources

 

Alignments for a candidate for cycA in Klebsiella michiganensis M5al

Align D-serine/D-alanine/glycine transporter (characterized)
to candidate BWI76_RS08745 BWI76_RS08745 proline-specific permease

Query= SwissProt::P0AAE0
         (470 letters)



>FitnessBrowser__Koxy:BWI76_RS08745
          Length = 459

 Score =  350 bits (897), Expect = e-101
 Identities = 177/451 (39%), Positives = 282/451 (62%), Gaps = 10/451 (2%)

Query: 19  LRRNLTNRHIQLIAIGGAIGTGLFMGSGKTISLAGPSIIFVYMIIGFMLFFVMRAMGELL 78
           L R L  RHI+ IA+G AIGTGLF GS   I  AGP+++  Y+I G  +F VMRA+GE+ 
Sbjct: 9   LLRGLNARHIRFIALGSAIGTGLFYGSASAIKAAGPAVLLAYLIGGAAVFIVMRALGEMA 68

Query: 79  LSNLEYKSFSDFASDLLGPWAGYFTGWTYWFCWVVTGMADVVAITAYAQFWFPDLSDWVA 138
           + N    SFS +A   LGP AG+ TGWTY F  V+  +ADV A   Y   W+PD+  W+ 
Sbjct: 69  VRNPVSGSFSSYARQYLGPLAGFITGWTYTFEMVIVALADVTAFGIYMGLWYPDVPRWIW 128

Query: 139 SLAVIVLLLTLNLATVKMFGEMEFWFAMIKIVAIVSLIVVGLVMVAMHFQS---PTGVEA 195
            L++I  +  +NL +V++FGEMEFW ++IK+VAI+++IV G  ++   F +    TG+E 
Sbjct: 129 VLSIIFFIGAMNLCSVRVFGEMEFWLSLIKVVAIIAMIVAGGSIIFFGFGNAFPATGLE- 187

Query: 196 SFAHLWNDGGWFPKGLSGFFAGFQIAVFAFVGIELVGTTAAETKDPEKSLPRAINSIPIR 255
              +LW+ GG+ P G  G  A   I +FAF G+E++G TAAE K+P+K +P+AIN+IP+R
Sbjct: 188 ---NLWSHGGFAPNGWEGIIASLGIVMFAFGGVEIIGVTAAEAKNPQKVIPQAINTIPLR 244

Query: 256 IIMFYVFALIVIMSVTPWSSVVPEKSPFVELFVLVGLPAAASVINFVVLTSAASSANSGV 315
           I++FYV  L ++M++ PW+S     SPFV +F  +G+PAAA+++N +V++++ S+ NS +
Sbjct: 245 IVLFYVCTLAILMAIFPWNSFGERGSPFVLIFDGLGIPAAATILNIIVISASISAINSDI 304

Query: 316 FSTSRMLFGLAQEGVAPKAFAKLSKRAVPAKGLTFSCICLLGGVVMLYVNPSVIGAFTMI 375
           F   RM++G+A+EG+APK+F +++   VP   +    + LL  VV+ Y+ P  +  F +I
Sbjct: 305 FGAGRMMYGMAKEGLAPKSFQRIASNGVPWMTVVVMGVALLAAVVLNYLMPEQV--FVLI 362

Query: 376 TTVSAILFMFVWTIILCSYLVYRKQRPHLHEKSI-YKMPLGKLMCWVCMAFFVFVVVLLT 434
            +++A   ++VW +IL ++   R+        +I + +PL  +   + + F   V+ +L 
Sbjct: 363 ASLAAFATVWVWVMILLAHFAMRRGLSAEERGNIAFPVPLWPVAPLLTLLFMGLVIAVLG 422

Query: 435 LEDDTRQALLVTPLWFIALGLGWLFIGKKRA 465
           + ++TR AL+   +W   L   W    +K A
Sbjct: 423 MVEETRIALIAGLVWLGLLTAVWFARVRKNA 453


Lambda     K      H
   0.329    0.141    0.440 

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: 642
Number of extensions: 34
Number of successful extensions: 3
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: 470
Length of database: 459
Length adjustment: 33
Effective length of query: 437
Effective length of database: 426
Effective search space:   186162
Effective search space used:   186162
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 (21.8 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