GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natD in Mesorhizobium ciceri WSM1271

Align NatD aka LivH aka SLR0949, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate YP_004144382.1 Mesci_5234 inner-membrane translocator

Query= TCDB::P74318
         (286 letters)



>NCBI__GCF_000185905.1:YP_004144382.1
          Length = 302

 Score =  172 bits (436), Expect = 8e-48
 Identities = 96/295 (32%), Positives = 170/295 (57%), Gaps = 18/295 (6%)

Query: 5   QLIFNGIAVGSIIALGAVGLTLTYGILRLSNFAHGDFMTLAAYLTWWANTS--------- 55
           Q + +G+  GS+I LGA+G+TLTY ILR SNFAHGDFM    Y T    ++         
Sbjct: 4   QFVVDGLLTGSMIGLGAIGVTLTYSILRFSNFAHGDFMAWGTYATLAVVSAIGATVGKVA 63

Query: 56  -------GINLWLSMALGCVGTIIAMFIGEWLLWKPMRARRATATTLIIISIGLALFLRN 108
                  G  L +++ +G   T +   + + +L+  +R++   A  +++ S G ++ LR+
Sbjct: 64  PIAPLSFGWPLIVALVVGMAFTALLALLLDKVLFSRLRSQ-GQAIIVVMASFGASMALRS 122

Query: 109 GILLIWGGNNQNYRVPIVPAQDF-MGIKFEYYRLLVIAMAIAAMVVLHLILQRTKVGKAM 167
            +   +      +   I  A     GI+    ++ ++ +    ++ +HL++ RT+ G++M
Sbjct: 123 LLEFTFTSRPTYFSRAIQIAMPVGFGIRITSDQIALLLLTAVLVLAVHLLMTRTQTGRSM 182

Query: 168 RAVADNVDLAKVSGINVEWVVMWTWVMTAVLTALGGSMYGLMTTLKPNMGWFLILPMFAS 227
           +A++ N  LA++ GI+V  VV  TWV+   L  + G M G++  ++P MG+ ++LPMFA+
Sbjct: 183 QALSQNAALARIVGIDVASVVRVTWVIGGALACVAGVMIGILVQIRPFMGFDMLLPMFAA 242

Query: 228 VILGGIGNPYGAIAGGIIIGVAQEVSVPWFGTSYKMGVALLLMIIILFIRPQGLF 282
            ILGGIG+  GA+ GG+IIG+A+  +V   G  ++  V+ ++++ +LF+RP GLF
Sbjct: 243 AILGGIGSIPGAVLGGLIIGLAEAGAVQLIGAEWRAAVSFIILMAVLFVRPIGLF 297


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: 201
Number of extensions: 9
Number of successful extensions: 3
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: 302
Length adjustment: 26
Effective length of query: 260
Effective length of database: 276
Effective search space:    71760
Effective search space used:    71760
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: 48 (23.1 bits)

This GapMind analysis is from Sep 24 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