GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AZOBR_RS08235 in Klebsiella michiganensis M5al

Align L-proline and D-alanine ABC transporter, permease component 1 (characterized)
to candidate BWI76_RS05990 BWI76_RS05990 branched-chain amino acid ABC transporter permease

Query= reanno::azobra:AZOBR_RS08235
         (301 letters)



>FitnessBrowser__Koxy:BWI76_RS05990
          Length = 299

 Score =  223 bits (569), Expect = 3e-63
 Identities = 123/299 (41%), Positives = 182/299 (60%), Gaps = 10/299 (3%)

Query: 4   FLQQLINGLSLGAIYGLIAIGYTMVYGIIGMINFAHGEIYMIGAFVALITFLAIGSLGIT 63
           FLQQ++NG+SLG +Y LIAIGYTMVYG++ +INFAH ++ M+GAF  L  F +IG     
Sbjct: 6   FLQQVVNGMSLGGMYALIAIGYTMVYGVLRLINFAHADVMMVGAFTTLFLFSSIG----- 60

Query: 64  WVPLALLVMLVASMLFTAVYGWTVERIAYRPLRSSPRLAPLISAIGMSIFLQNYVQILQG 123
            +P  + V L  ++    ++G  ++R+AYRPLR + +++ LI+AIG+S FL+N   +L G
Sbjct: 61  -LPFGVAVFLTLALC--GLFGMLIDRVAYRPLRQASKISMLITAIGVSFFLENLFNVLFG 117

Query: 124 ARSKPLQPILPGNLTLMDGAVSVSYVRLATIVITIALMYGFTQLITRTSLGRAQRACEQD 183
             S+        N T   G V ++ V     +IT+ L+     L+ RT  G A RA   D
Sbjct: 118 GSSRFFSAPDFFNNTRAFGDVIITNVAWIVPLITVLLLLAILWLLYRTRYGMAIRAVAFD 177

Query: 184 KKMAGLLGVNVDRVISLTFVMGAALAAVAGMMVLLIYGVIDFYIGFLAGVKAFTAAVLGG 243
                L+G++ +R+ISL F +G++LAA+ G+   + Y  ID  +G L G+KAF AAVLGG
Sbjct: 178 VNTVRLMGIDANRIISLVFALGSSLAALGGVFYSISYPTIDPLMGVLIGLKAFAAAVLGG 237

Query: 244 IGSLPGAMLGGVVIGLIEAFWSGYMG--SEWKDVATFTILVLVLIFRPTGLLGRPEIEK 300
           IGS+ GA+LGG ++G  E            +KD   F  L+LVL+FRP G++G   +E+
Sbjct: 238 IGSVTGAVLGGFILGFTEVVAVALFPELGGYKDAFAFMFLILVLLFRPVGIMGDERLER 296


Lambda     K      H
   0.329    0.144    0.425 

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: 339
Number of extensions: 25
Number of successful extensions: 5
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: 301
Length of database: 299
Length adjustment: 27
Effective length of query: 274
Effective length of database: 272
Effective search space:    74528
Effective search space used:    74528
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: 48 (23.1 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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