GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PS417_11895 in Klebsiella michiganensis M5al

Align m-Inositol ABC transporter, permease component (iatP) (characterized)
to candidate BWI76_RS19635 BWI76_RS19635 galactoside ABC transporter permease MglC

Query= reanno::pseudo3_N2E3:AO353_21390
         (340 letters)



>FitnessBrowser__Koxy:BWI76_RS19635
          Length = 336

 Score =  202 bits (515), Expect = 8e-57
 Identities = 111/307 (36%), Positives = 180/307 (58%), Gaps = 13/307 (4%)

Query: 43  IVRDQSFLMNSQRLVLMILQVSIIGLLAIGVTQVIITTGIDLSSGSVLALSAMIAASLAQ 102
           I +D +FL +   L  ++ Q S+  ++A+GV  +I+T G DLS+G  + L+A+IAA++ Q
Sbjct: 30  IFQDPTFL-SLLNLSNILTQSSVRIIIALGVAGLIVTQGTDLSAGRQVGLAAVIAATMLQ 88

Query: 103 TSDFARAVFPSLTDLPVWIPVIAGLGVGLLAGAINGSIIAVTGIPPFIATLGMMVSARGL 162
             D A  VFP +  +P+ + ++    +G + G ING IIA   + PFI TLG M+   G+
Sbjct: 89  AVDNANKVFPEMATMPIPLVILLVCAIGAVIGLINGIIIAYLNVTPFITTLGTMIIVYGI 148

Query: 163 ARYYTE---GQPVS-------MLSDSYTAIGHGAMPVIIFLVVAVIFHIALRY--TKYGK 210
              Y +     P+S         +  + A+G   +  I F  +  +F + + +  T++GK
Sbjct: 149 NSLYYDFVGASPISGFDSHFSQFAQGFVALGSFRLSYITFYALIAVFFVWILWNKTRFGK 208

Query: 211 YTYAIGGNMQAARTSGINVKRHLVIVYSIAGLLAGLAGVVASARAATGQAGMGMSYELDA 270
             +AIGGN +AA+ SG+NV  +L+++Y+++G+     G++ + R  +    +G  YELDA
Sbjct: 209 NIFAIGGNPEAAKVSGVNVALNLLMIYALSGVFYAFGGLLEAGRIGSATNNLGFMYELDA 268

Query: 271 IAAAVIGGTSLAGGVGRITGTVIGALILGVMASGFTFVGVDAYIQDIIKGLIIVIAVVID 330
           IAA V+GG S +GGVG + G V G +I  V+  G T++GV+ Y Q IIKG II+ AV +D
Sbjct: 269 IAACVVGGVSFSGGVGTVFGVVTGVIIFTVINYGLTYIGVNPYWQYIIKGAIIIFAVALD 328

Query: 331 QYRNKRK 337
             +  RK
Sbjct: 329 SLKYARK 335


Lambda     K      H
   0.326    0.140    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: 260
Number of extensions: 13
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: 340
Length of database: 336
Length adjustment: 28
Effective length of query: 312
Effective length of database: 308
Effective search space:    96096
Effective search space used:    96096
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 49 (23.5 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