GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natD in Pseudomonas fluorescens FW300-N2C3

Align NatD aka LivH aka SLR0949, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate AO356_08495 AO356_08495 branched-chain amino acid transporter permease subunit LivH

Query= TCDB::P74318
         (286 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_08495
          Length = 304

 Score =  135 bits (341), Expect = 9e-37
 Identities = 90/291 (30%), Positives = 156/291 (53%), Gaps = 16/291 (5%)

Query: 5   QLIFNGIAVGSIIALGAVGLTLTYGILRLSNFAHGDFMTLAAYLTWWANTS----GINLW 60
           Q + NG+ +GS+  L A+G T+ YGI+ + NFAHG+   ++AYL   +       GI  +
Sbjct: 7   QQLINGLTLGSVYGLIAIGYTMVYGIIGMINFAHGEVYMISAYLAAISLALLAYFGIESF 66

Query: 61  LSMALGC-VGTIIAMFIGEWLL----WKPMRARRATATTLIIISIGLALFLRNGILLIWG 115
             M LG  V TI+   +  W++    +KP+R   +T    +I +IG++L L+N   +  G
Sbjct: 67  PLMILGTLVFTIVVTGVYGWVIERVAYKPLR--NSTRLAPLISAIGISLILQNYAQISQG 124

Query: 116 GNNQNYRVPIVPAQDF-MG---IKFEYYRLLVIAMAIAAMVVLHLILQRTKVGKAMRAVA 171
              Q     +  A  F  G   ++  Y ++ ++  A A M VL  I++ TK+G+  RA  
Sbjct: 125 ARQQGVPTLLEGAMRFDFGSGFVQLTYTKIFILIAAFAGMGVLTYIIKYTKLGRMCRATQ 184

Query: 172 DNVDLAKVSGINVEWVVMWTWVMTAVLTALGGSMYGL-MTTLKPNMGWFLILPMFASVIL 230
            +  +A + GIN + V+ + +++ A + AL G +  +   T     G+ + +  F + +L
Sbjct: 185 QDRKMASILGINTDRVISYVFIIGAAMAALAGVLITMNYGTFDFYAGFIIGIKAFTAAVL 244

Query: 231 GGIGNPYGAIAGGIIIGVAQEVSVPWFGTSYKMGVALLLMIIILFIRPQGL 281
           GGIG+  GA+ GGII+G+++ +      + YK   +  L+++IL  RPQGL
Sbjct: 245 GGIGSLPGAMLGGIILGISESLFSGLINSDYKDVFSFSLLVLILIFRPQGL 295


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: 212
Number of extensions: 13
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: 304
Length adjustment: 26
Effective length of query: 260
Effective length of database: 278
Effective search space:    72280
Effective search space used:    72280
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 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