GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braD in Klebsiella michiganensis M5al

Align High-affinity branched-chain amino acid transport system permease protein BraD, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)
to candidate BWI76_RS05990 BWI76_RS05990 branched-chain amino acid ABC transporter permease

Query= TCDB::P21627
         (307 letters)



>FitnessBrowser__Koxy:BWI76_RS05990
          Length = 299

 Score =  227 bits (579), Expect = 2e-64
 Identities = 131/308 (42%), Positives = 191/308 (62%), Gaps = 25/308 (8%)

Query: 7   YLQQLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYIAFIAITLLAMMGLD 66
           +LQQ+VNG+++G  YALIAIGYTMVYG++ +INFAH +V M+G   AF  + L + +GL 
Sbjct: 6   FLQQVVNGMSLGGMYALIAIGYTMVYGVLRLINFAHADVMMVG---AFTTLFLFSSIGLP 62

Query: 67  SVPLMMLAAFAASIIVTSA----FGYSIERVAYRPLRGGNRLIPLISAIGMSIFLQNA-- 120
                    F  ++ +T A    FG  I+RVAYRPLR  +++  LI+AIG+S FL+N   
Sbjct: 63  ---------FGVAVFLTLALCGLFGMLIDRVAYRPLRQASKISMLITAIGVSFFLENLFN 113

Query: 121 VMLSQDSKEKAIPTLLPGNFVFGESSMNGVVISYMQILIFVVTFLVMFGLTLFISRSRLG 180
           V+    S+  + P        FG+     V+I+ +  ++ ++T L++  +   + R+R G
Sbjct: 114 VLFGGSSRFFSAPDFFNNTRAFGD-----VIITNVAWIVPLITVLLLLAILWLLYRTRYG 168

Query: 181 RACRACAEDLKMTNLLGINSNNIIALTFVIGAALAAVAAVLLGMQYGVINPGIGFLAGIK 240
            A RA A D+    L+GI++N II+L F +G++LAA+  V   + Y  I+P +G L G+K
Sbjct: 169 MAIRAVAFDVNTVRLMGIDANRIISLVFALGSSLAALGGVFYSISYPTIDPLMGVLIGLK 228

Query: 241 AFTAAVLGGIGSIPGAMLGGLLLGVAEAFGADVFGD--QYKDVVAFGLLILVLLFRPTGI 298
           AF AAVLGGIGS+ GA+LGG +LG  E     +F +   YKD  AF  LILVLLFRP GI
Sbjct: 229 AFAAAVLGGIGSVTGAVLGGFILGFTEVVAVALFPELGGYKDAFAFMFLILVLLFRPVGI 288

Query: 299 LGRPEVEK 306
           +G   +E+
Sbjct: 289 MGDERLER 296


Lambda     K      H
   0.328    0.145    0.413 

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: 321
Number of extensions: 18
Number of successful extensions: 6
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: 307
Length of database: 299
Length adjustment: 27
Effective length of query: 280
Effective length of database: 272
Effective search space:    76160
Effective search space used:    76160
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 (21.7 bits)
S2: 48 (23.1 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