GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natD in Sinorhizobium meliloti 1021

Align NatD aka LivH aka SLR0949, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate SM_b20604 SM_b20604 branched-chain amino acid ABC transporter permease

Query= TCDB::P74318
         (286 letters)



>FitnessBrowser__Smeli:SM_b20604
          Length = 537

 Score =  133 bits (335), Expect = 8e-36
 Identities = 90/296 (30%), Positives = 153/296 (51%), Gaps = 28/296 (9%)

Query: 5   QLIFNGIAVGSIIALGAVGLTLTYGILRLSNFAHGDFMTLAAYLTWWAN----TSGINLW 60
           Q I+ G+++GS++ L A+GL +T+G++ + N AHG+ + L AY T+       TS  +L+
Sbjct: 243 QNIWYGLSLGSVLLLAAIGLAITFGVMGIINMAHGEMVMLGAYTTFLVQDVVRTSFPHLF 302

Query: 61  ---LSMAL-------GCVGTIIAMFIGEWLLWKPMRARRATATTLIIISIGLALFLRNGI 110
              L++AL       G VG  +   +  +L  +P+    AT         G++L L+  +
Sbjct: 303 EWSLAIALPLAFLVTGAVGLALERGVIRFLYGRPLETLLATW--------GISLILQQTV 354

Query: 111 LLIWGGNNQNYRVP--IVPAQDFMGIKFEYYRLLVIAMAIAAMVVLHLILQRTKVGKAMR 168
             I+G  N+    P  +  A +  G+   + RL +I  A+A    L  +L++T +G  MR
Sbjct: 355 RTIFGPTNREVGNPSWMSGAFELGGLAITWNRLWIIVFALAVFAALLFLLKKTPMGLQMR 414

Query: 169 AVADNVDLAKVSGINVEWVVMWTWVMTAVLTALGGSMYGLMTTLKPNMGWFLILPMFASV 228
           AV  N  +A   GI   WV   T+ + + +  + G     +  + PN+G   I+  F  V
Sbjct: 415 AVTQNRRMASSMGIRTPWVDALTFALGSGIAGIAGVALSQIDNVSPNLGQGYIIDSFMVV 474

Query: 229 ILGGIGNPYGAIAGGIIIGVAQEVSVPWFGTSYKMGVALLLMIIILFI--RPQGLF 282
           + GG+GN +G + G   +G+  +   P+ G    +G  L+L++IILFI  RP+GLF
Sbjct: 475 VFGGVGNLWGTLVGAFSLGILNKFLEPYAGA--VLGKILVLVLIILFIQKRPRGLF 528


Lambda     K      H
   0.329    0.143    0.450 

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: 380
Number of extensions: 17
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: 286
Length of database: 537
Length adjustment: 31
Effective length of query: 255
Effective length of database: 506
Effective search space:   129030
Effective search space used:   129030
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: 50 (23.9 bits)

This GapMind analysis is from Apr 09 2024. 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