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_RS07280 BWI76_RS07280 branched-chain amino acid ABC transporter permease

Query= TCDB::P21627
         (307 letters)



>FitnessBrowser__Koxy:BWI76_RS07280
          Length = 316

 Score =  243 bits (619), Expect = 6e-69
 Identities = 137/305 (44%), Positives = 187/305 (61%), Gaps = 12/305 (3%)

Query: 8   LQQLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYIAFIAITLLAMMGLDS 67
           +QQ++NG+ +GS YALIA+GYTMVYGI+ +INFAHG++ M+G+      +  L       
Sbjct: 5   IQQIINGVMLGSIYALIALGYTMVYGILRIINFAHGDILMVGALTTLSGMHALNAHFPTL 64

Query: 68  VPLMMLA-AFAASIIVTSAFGYSIERVAYRPLRGGNRLIPLISAIGMSIFLQNAVMLSQD 126
            PL  L  A   ++ V +    ++ER AYR LR   RL PLIS IG+S+ LQ   M+   
Sbjct: 65  PPLAQLGLALLLAMTVCALLAMAVERFAYRRLRNAPRLAPLISGIGVSVLLQTVAMIVWS 124

Query: 127 SKEKAIPTLLPGNFV---FGESSMNGVVISYMQILIFVVTFLVMFGLTLFISRSRLGRAC 183
                 P +LP + +    G ++    +I+   I+   +   VM GL L +  +RLGR  
Sbjct: 125 RNPLMFPQILPMDPIAVTHGSAAHPPALITVTGIVTVALALTVMLGLWLLVEYTRLGRGM 184

Query: 184 RACAEDLKMTNLLGINSNNIIALTFVIGAALAAVAAVLLGMQYGVINPGIGFLAGIKAFT 243
           RA AE+ ++  L+G+N N IIALTF IG   AA+A V++   YG     +GFL GIKAFT
Sbjct: 185 RAVAENPRIATLMGVNPNAIIALTFAIGGVFAALAGVMMASNYGSAGFSMGFLPGIKAFT 244

Query: 244 AAVLGGIGSIPGAMLGGLLLGVAEAFGA--------DVFGDQYKDVVAFGLLILVLLFRP 295
           AAVLGGIG+I GAM+GGLLLG+ E+ GA         VFG  Y+D+ AF +LILVL+FRP
Sbjct: 245 AAVLGGIGNIRGAMIGGLLLGLIESLGAGYLGDLTHGVFGSNYQDIFAFMVLILVLVFRP 304

Query: 296 TGILG 300
            G+LG
Sbjct: 305 AGLLG 309


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: 302
Number of extensions: 12
Number of successful extensions: 4
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: 316
Length adjustment: 27
Effective length of query: 280
Effective length of database: 289
Effective search space:    80920
Effective search space used:    80920
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