GapMind for catabolism of small carbon sources

 

Aligments for a candidate for AZOBR_RS08260 in Klebsiella michiganensis M5al

Align Branched-chain amino acid ABC transporter,substrate-binding periplasmic component (characterized, see rationale)
to candidate BWI76_RS07260 BWI76_RS07260 branched chain amino acid ABC transporter substrate-binding protein

Query= uniprot:G8ALJ3
         (366 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS07260 BWI76_RS07260 branched chain
           amino acid ABC transporter substrate-binding protein
          Length = 385

 Score =  205 bits (521), Expect = 2e-57
 Identities = 115/362 (31%), Positives = 199/362 (54%), Gaps = 5/362 (1%)

Query: 6   SLLVAVAATAMTASVAKADIAVATAGPITGQYATFGEQMKKGIEQAVADINAAGGVLGQK 65
           ++L++  A++   S A   + +  AGP+TG  A  G+ ++ G + A+ DIN     +G K
Sbjct: 12  AILLSGFASSAAWSAASETVIIGLAGPLTGPSARIGKDLENGAQLAIDDINKQHPTIGGK 71

Query: 66  ---LKLEVGDDACDPKQAVAVANQLAKAGVKFVAGHFCSGSSIPASQVYAEEGVLQISPA 122
               KL+  DD  DP+ AVAVA +L  +GV  V GH+ +G+SIPA++VY + G+ Q++P 
Sbjct: 72  AVTFKLQSEDDQSDPRTAVAVAQRLVDSGVAGVVGHWNTGTSIPAARVYHDAGIAQVAPV 131

Query: 123 STNPKLTEQNLKNVFRVCGRDDQQGQIAGKYLLENYKGKNVAILHDKSAYGKGLADETQK 182
           +T    T+Q     FRV G DD  GQ AG+Y ++  K K +A++ D++A+G+GLADE  K
Sbjct: 132 ATGHAYTKQGFDTSFRVMGHDDDGGQFAGQYAVQTLKAKRIAVIDDRTAFGQGLADEFIK 191

Query: 183 ALNAGGQKEKIYEAYTAGEKDYSALVSKLKQEAVDVVYVGGYHTEAGLLARQMKDQGLNA 242
           +L   G      +       D+SA+++ ++ +  D+++ GG  ++A  LAR++K  G+NA
Sbjct: 192 SLEVQGINIVDRQYVDDKTVDFSAVLTAIRSKNADLIFFGGVDSQAAPLARRIKQLGMNA 251

Query: 243 PIVSGDALVTNEYWAITGPAGENTMMTFGPDPREMPEAKEAVEKFRKAGYEP--EGYTLY 300
            ++     V+  +  +    G+  +      P E     +A E+  ++ Y    E +  +
Sbjct: 252 TLMGAGGFVSQTFLQLAQKEGDGVVALEPGLPVERMPGGKAFEQAYQSRYHTHIELHAPF 311

Query: 301 TYAALQIWAEAAKQANSTDSAKIADVLRKNSYNTVIGKIGFDAKGDVTSPAYVWYRWNNG 360
            Y A ++   A ++A+S D A     LR  +Y  V G+I FD +G++ SP +  Y+   G
Sbjct: 312 AYDATRVLVAAMEKADSVDPADYLPALRAINYAGVTGQIAFDKEGNLKSPTFTVYKVVEG 371

Query: 361 QY 362
           ++
Sbjct: 372 KW 373


Lambda     K      H
   0.312    0.129    0.366 

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: 350
Number of extensions: 16
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: 366
Length of database: 385
Length adjustment: 30
Effective length of query: 336
Effective length of database: 355
Effective search space:   119280
Effective search space used:   119280
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 50 (23.9 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, the preprint on GapMind for carbon sources, 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