GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PS417_17590 in Klebsiella michiganensis M5al

Align ABC transporter substrate-binding protein; SubName: Full=Histidine transport system substrate-binding protein (characterized, see rationale)
to candidate BWI76_RS19240 BWI76_RS19240 ABC transporter substrate-binding protein

Query= uniprot:A0A1N7UK26
         (258 letters)



>FitnessBrowser__Koxy:BWI76_RS19240
          Length = 257

 Score =  201 bits (512), Expect = 1e-56
 Identities = 109/251 (43%), Positives = 153/251 (60%), Gaps = 4/251 (1%)

Query: 9   AALL--LPLCATAHAQEWKEIRFGVFPEYPPFESVAADGSLQGFDIELGNAICAKLEVKC 66
           AALL  + L A   AQ++  I FGV   YPPF+ +A  G + GFDI++ NA+C +L+ KC
Sbjct: 6   AALLACMALSAPLAAQQFDTISFGVDGGYPPFDVLAPSGEITGFDIDIANALCTQLKAKC 65

Query: 67  TWVHNEFDGMIPALRARKFDAIMSSMAVTPAREKIIDFSDRLFLSPTSVITRKSADFGDT 126
            +V   F+ MI AL A KFDAI++S+ +T  R+K +DF+DR + S   ++ RK +     
Sbjct: 66  VFVKQPFESMIAALNAHKFDAIIASLNITDERKKEVDFTDRYYRSAAQLVARKGSPLLPD 125

Query: 127 PESLMGKQVGVLQGSLQEAYARAHLAKLGAQIKAYQSQDQNYADLQNGRLDATLTDKLEA 186
             SL GK VGV  GS  EA+A+A+ A  G +I  Y +QD  Y DL +GR+DA L D ++A
Sbjct: 126 AASLKGKTVGVQTGSTHEAFAKANWANHGVKIVGYANQDNVYLDLLSGRIDAALQDNIQA 185

Query: 187 QLNFLSKPEGSDFK-TGPAFKDPTLPLDIAMGLRKNDQALRALINKGIAAVQADGTYAQI 245
              F+  P G  F   GP  +D  +  D+ + + K++ ALR  +N  I A++ADGTY  I
Sbjct: 186 ATGFIDTPRGQKFAFAGPVIQDGGISSDVGIAVNKDNPALRDALNGAIKAIRADGTYDAI 245

Query: 246 QKKYFGDQDIY 256
           QKKYF   DIY
Sbjct: 246 QKKYF-SFDIY 255


Lambda     K      H
   0.319    0.135    0.393 

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: 174
Number of extensions: 8
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: 258
Length of database: 257
Length adjustment: 24
Effective length of query: 234
Effective length of database: 233
Effective search space:    54522
Effective search space used:    54522
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 (21.8 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:

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