GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_03045 in Klebsiella michiganensis M5al

Align ABC transporter for L-Arginine and L-Citrulline, permease component 1 (characterized)
to candidate BWI76_RS19230 BWI76_RS19230 polar amino acid ABC transporter inner membrane subunit

Query= reanno::pseudo3_N2E3:AO353_03045
         (232 letters)



>FitnessBrowser__Koxy:BWI76_RS19230
          Length = 241

 Score =  169 bits (428), Expect = 4e-47
 Identities = 87/215 (40%), Positives = 131/215 (60%), Gaps = 5/215 (2%)

Query: 18  GLVTTLKLLALSLLFGLLAALPLGLMRVSKQPIVNMSAWLYTYVIRGTPMLVQLFLIYYG 77
           GL  T +L  LS++ G+  A+ + + +V     + +    +TY  R TP+ +QL LIYYG
Sbjct: 24  GLAVTAELFLLSIVPGMALAIAMAVGQVYGPRGLALPIRAFTYFFRSTPLYLQLMLIYYG 83

Query: 78  LAQFEAVRESFL-----WPWLSSATFCACLAFAINTSAYTAEIIAGSLRATPNGEIEAAK 132
           L+QF+ V+  ++     W     ATFCA LA  +NT+AY AE++AG +   P  E  A +
Sbjct: 84  LSQFDIVQTGWMNDQPFWLLFRDATFCATLALVLNTAAYVAELLAGMMVTFPRQEWIAGE 143

Query: 133 AMGMSRFKMYKRILLPSALRRALPQYSNEVIMMLQTTSLASIVTLIDITGAARTVNAQYY 192
           A GM ++++ +R++LP+ LRR +P  +NE++ +L  TSLAS VTL+DITG AR   A  Y
Sbjct: 144 AYGMGKWQIIRRLVLPATLRRGIPALNNEMVFLLHATSLASTVTLLDITGVARAFYAMTY 203

Query: 193 LPFEAYITAGVFYLCMTFILVRLFKMAEHRWLGYL 227
            PF  ++ A   YL  TF+L+  F  AE RWL ++
Sbjct: 204 SPFIPFLMAAALYLLCTFLLIFTFARAERRWLAFI 238


Lambda     K      H
   0.329    0.139    0.427 

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: 190
Number of extensions: 12
Number of successful extensions: 2
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: 232
Length of database: 241
Length adjustment: 23
Effective length of query: 209
Effective length of database: 218
Effective search space:    45562
Effective search space used:    45562
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: 46 (22.3 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