GapMind for catabolism of small carbon sources

 

Aligments for a candidate for HSERO_RS00885 in Klebsiella michiganensis M5al

Align ABC transporter permease (characterized, see rationale)
to candidate BWI76_RS26345 BWI76_RS26345 branched-chain amino acid ABC transporter permease LivH

Query= uniprot:A0A165KC95
         (309 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS26345 BWI76_RS26345 branched-chain
           amino acid ABC transporter permease LivH
          Length = 308

 Score =  246 bits (628), Expect = 5e-70
 Identities = 135/305 (44%), Positives = 197/305 (64%), Gaps = 19/305 (6%)

Query: 5   LQQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIG--MMQGAMP 62
           LQQ+ NG+ LGS YALIA+GYTMVYGII +INFAHGEV MIG+  S+  I   MM G   
Sbjct: 9   LQQMFNGVTLGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVSFMIIAALMMMGI-- 66

Query: 63  GAPGWVILLLATIIACVVAATLNFVIEKVAYRPLRSSPRLAPLITAIGMSILLQTLAMII 122
               W+++    + A V+A+   + IE+VAYRP+RSS RL  LI+AIGMSI LQ    + 
Sbjct: 67  -DTSWLLVAAGFVGAIVIASAYGWSIERVAYRPVRSSKRLIALISAIGMSIFLQNYVSLT 125

Query: 123 WKPNYKPYPTMLPSSPFEIGG-----AFITPTQILILGVTAVALASLVYLVNHTNLGRAM 177
                   P++  +  + +G      A IT  Q++I  VT +A+ +L   + ++ +GRA 
Sbjct: 126 EGSRDVALPSLF-NGQWTVGSSDNFSATITTMQLVIWVVTFIAMLALTLFIRYSRMGRAC 184

Query: 178 RATAENPRVASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGLKAFT 237
           RA AE+ ++ASL+G+  D VI+ TF+IGA +AA+AG++    YG     +GF+ G+KAFT
Sbjct: 185 RACAEDLKMASLLGINTDRVIALTFVIGAAMAAVAGVLLGQFYGVINPYIGFMAGMKAFT 244

Query: 238 AAVFGGIGNLAGAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIILTLRP 297
           AAV GGIG++ GA++GG++LG+ EA+ S Y+ T         Y D+ +F +LI++L + P
Sbjct: 245 AAVLGGIGSIPGAMIGGLILGIAEALSSAYLST--------EYKDVVSFALLILVLLVMP 296

Query: 298 SGLLG 302
           +G+LG
Sbjct: 297 TGILG 301


Lambda     K      H
   0.327    0.142    0.419 

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: 254
Number of extensions: 10
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: 309
Length of database: 308
Length adjustment: 27
Effective length of query: 282
Effective length of database: 281
Effective search space:    79242
Effective search space used:    79242
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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