GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_2555 in Klebsiella michiganensis M5al

Align ABC transporter for L-Histidine, periplasmic substrate-binding component 1 (characterized)
to candidate BWI76_RS08975 BWI76_RS08975 amino acid ABC transporter substrate-binding protein

Query= reanno::acidovorax_3H11:Ac3H11_2555
         (249 letters)



>FitnessBrowser__Koxy:BWI76_RS08975
          Length = 248

 Score =  160 bits (406), Expect = 2e-44
 Identities = 91/242 (37%), Positives = 130/242 (53%), Gaps = 3/242 (1%)

Query: 5   RNLLLASLAAAAFC-TTGAQAQDNVLRVGTDATFPPMEFVENGKRTGFDIELVEAIAKTM 63
           +++   SLAA        + A D  L V TD  F P EF +  K  GFD++L  AIAK +
Sbjct: 2   KSVFKVSLAALTLAFAVSSHAADKKLVVATDTAFVPFEFKQGDKYVGFDVDLWAAIAKEL 61

Query: 64  GKQVEWVDIDFKGLIPGLISKRFDMAVSAIYITDERKKVVDFTDSYYAGGLVVMVKADNK 123
                   +DF G+IP L +K  D+A++ I ITDERKK +DF+D YY  GL+VMV A+N 
Sbjct: 62  KLDYTLKPMDFSGIIPALQTKNIDLALAGITITDERKKAIDFSDGYYKSGLLVMVNANNN 121

Query: 124 AINKLADLDGKKVSVQVGTKSVSYLTEKFPKVQRVEVEKNQEMFNLVDIGRADAAVTGKP 183
            I  + DL+GK V+V+ GT SV Y           +       +  +  GRADA +   P
Sbjct: 122 DIKDVKDLNGKVVAVKGGTGSVDYAKANIKTKDLRQFPNIDNAYMELGTGRADAVLHDTP 181

Query: 184 AAFQYVRTRPG--LRVLDEQLTTEEYGMALRKDTPELTKAVNGAITKLKADGTYAAIVKK 241
               +++T      + + + L  + YG+A  K + EL + VNGA+  L+ +GTY  I KK
Sbjct: 182 NILYFIKTAGNGKFKAVGDSLEAQNYGIAFPKGSDELREKVNGALKTLRENGTYNEIYKK 241

Query: 242 WF 243
           WF
Sbjct: 242 WF 243


Lambda     K      H
   0.317    0.133    0.369 

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: 158
Number of extensions: 5
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: 249
Length of database: 248
Length adjustment: 24
Effective length of query: 225
Effective length of database: 224
Effective search space:    50400
Effective search space used:    50400
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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