GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natE in Marinobacter adhaerens HP15

Align NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate GFF2759 HP15_2703 branched-chain amino acid ABC transporter ATP-binding protein

Query= TCDB::P73650
         (240 letters)



>FitnessBrowser__Marino:GFF2759
          Length = 454

 Score =  200 bits (509), Expect = 4e-56
 Identities = 107/235 (45%), Positives = 156/235 (66%), Gaps = 3/235 (1%)

Query: 3   DLLVVKDVFAGYVADVPILQGINFSIAPGELVTVIGPNGAGKSTLAKTIFGLLTPSQGEI 62
           ++L +K +   Y   + +L  ++  I  GE+V+++G NGAGKSTL  TI GL    +G I
Sbjct: 220 EMLSIKGLVTSY-GQIEVLHDVDIHINSGEIVSLVGANGAGKSTLLMTISGLQPTDRGAI 278

Query: 63  IFKGENITGLGSDQIVRRGMCYVPQVCNVFGSLTVAENLDMGAFLHQGPTQTLKD--RIY 120
            F+G++++ + +DQ V  G+  VP+   VF  L+V +NL +GA+      + + D  R+Y
Sbjct: 279 TFEGKDLSKITADQRVADGIVQVPEGRQVFKDLSVHDNLLLGAYTRGKTPEVMDDLERMY 338

Query: 121 TMFPKLAQRRNQRAGTLSGGERQMLAMGRALMLDPDLLLLDEPSAALSPILVKDVFAQIK 180
           T FP L Q+R+  AG LSGG++QMLAMGRALM  P LLLLDEPS  L+P++++++F  +K
Sbjct: 339 TKFPILRQKRHNLAGELSGGQQQMLAMGRALMAKPRLLLLDEPSMGLAPLIIEEIFNIVK 398

Query: 181 AINATGKAIILVEQNAKQALMMADRGYVLENGRDKLEGSGQSLLNDPLVGELYLG 235
            +   G  I LVEQNA QAL +ADRGYVLE G+  +EG+G+ LL++  V E YLG
Sbjct: 399 ELKEEGITIFLVEQNASQALALADRGYVLETGKVVIEGTGRELLSNEKVREAYLG 453


Lambda     K      H
   0.320    0.139    0.393 

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: 260
Number of extensions: 13
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: 240
Length of database: 454
Length adjustment: 28
Effective length of query: 212
Effective length of database: 426
Effective search space:    90312
Effective search space used:    90312
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 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