GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natD in Paraburkholderia bryophila 376MFSha3.1

Align NatD aka LivH aka SLR0949, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate H281DRAFT_04062 H281DRAFT_04062 amino acid/amide ABC transporter membrane protein 1, HAAT family

Query= TCDB::P74318
         (286 letters)



>FitnessBrowser__Burk376:H281DRAFT_04062
          Length = 316

 Score =  139 bits (349), Expect = 1e-37
 Identities = 93/307 (30%), Positives = 166/307 (54%), Gaps = 35/307 (11%)

Query: 5   QLIFNGIAVGSIIALGAVGLTLTYGILRLSNFAHGDFMTLAAYLTWWA------NTSGIN 58
           Q I NG+ +GS+ A+ A+G T+ YGIL + NFAHGD + + A +   A      +  G+ 
Sbjct: 6   QQILNGLVLGSVYAIIALGYTMVYGILGIINFAHGDVLMVGAMVALSAIGVLQNHFPGLG 65

Query: 59  ----LWLSMALGCVGTIIAMFIGEWLLWKPMRARRATATTLIIISIGLALFLRNGILLIW 114
               L +++A+  V   +  +  E + ++P+R  +A     +I +IG+++ L+   ++IW
Sbjct: 66  NVPTLCIALAIAAVVCAVVGYTIERVAYRPLR--KAPRLAPLITAIGVSILLQTLAMMIW 123

Query: 115 GGNNQNYR-------VPIVPAQDFM-GIKFEYYRLLVIAMAIAAMVVLHLILQRTKVGKA 166
             N   +        + ++ A D   G       +++I +A   M  L L++ +TK+G+A
Sbjct: 124 SRNPLPFPQLLPTDPLNVIKATDTTPGAVISMTEIVIIVVAFLVMAGLLLLVHKTKLGRA 183

Query: 167 MRAVADNVDLAKVSGINVEWVVMWTWVMTAVLTALGGSM----YGLMTTLKPNMGWFLIL 222
           MRA+A+N  +A + G+N  +V+  T+++ + L AL G M    YG        MG+   L
Sbjct: 184 MRAIAENPGVASLMGVNPNFVISATFMIGSALAALAGVMIASEYG---NAHFYMGFIPGL 240

Query: 223 PMFASVILGGIGNPYGAIAGGIIIGVAQEVSVPW--------FGTSYKMGVALLLMIIIL 274
             F + +LGGIGN  GA+ GG+I+G+ +++   +        FG++Y+   A +++II+L
Sbjct: 241 KAFTAAVLGGIGNLGGAMVGGVILGLIEQLGAGYIGNLTGGVFGSNYQDVFAFIVLIIVL 300

Query: 275 FIRPQGL 281
             RP GL
Sbjct: 301 VFRPSGL 307


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: 213
Number of extensions: 14
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: 316
Length adjustment: 27
Effective length of query: 259
Effective length of database: 289
Effective search space:    74851
Effective search space used:    74851
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