GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braD in Phaeobacter inhibens BS107

Align NatD aka LivH aka SLR0949, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate GFF1572 PGA1_c15940 putative branched-chain amino acid transport system, permease protein

Query= TCDB::P74318
         (286 letters)



>FitnessBrowser__Phaeo:GFF1572
          Length = 336

 Score =  187 bits (476), Expect = 2e-52
 Identities = 110/316 (34%), Positives = 178/316 (56%), Gaps = 43/316 (13%)

Query: 11  IAVGSIIALGAVGLTLTYGILRLSNFAHGDFMTLAAYLT----WWANTSGINLW------ 60
           IA GS +ALGA+G+TL Y +LR SNFAHGD M     +T    WW  + GI+        
Sbjct: 19  IAYGSQLALGALGVTLIYSVLRFSNFAHGDTMAFGTMITILVTWWFQSMGISFGPLPTAL 78

Query: 61  LSMALGCVGTIIAMFIGEWLLWKPMRARRATATTLIIISIGLALFLRNGIL-LIWGGNNQ 119
           L++ +G  G ++ M I +  +++  RA++A     +++S+G+ +F+ NG++  I G  +Q
Sbjct: 79  LALPIGIAGCMLLMLITDRTVYRFYRAQKAKPVIFVMVSLGV-MFMMNGLVRFIIGPGDQ 137

Query: 120 NYRVP---IVPAQDFM-------GIKFEYYRLLVIAMAIAAMVVLHLILQRTKVGKAMRA 169
            +      I+ A+DF        G+  +  + + +  A+  + +L   L +T+ GK+MRA
Sbjct: 138 RFADGERFIISARDFKALTGLREGLAIKTTQGITVITAVVVVALLFWFLNKTRTGKSMRA 197

Query: 170 VADNVDLAKVSGINVEWVVMWTWVMTAVLTALGGSMYGLMTTLKPNMGWFLILPMFASVI 229
            +DN DLA +SGIN E VVM+TW++ A L  + G +YGL  + KP   + L+LP+FA+ I
Sbjct: 198 YSDNEDLALLSGINPERVVMYTWLIVATLATIAGVLYGLDKSFKPFTYFQLLLPIFAAAI 257

Query: 230 LGGIGNPYGAIAGGIIIGVAQ-EVSVPW--------------------FGTSYKMGVALL 268
           +GG+G+P GAIAGG II  ++  ++  W                      T YK  V+  
Sbjct: 258 VGGLGSPVGAIAGGFIIAFSEVTITYAWKKVLTYVVPETMKPDGLVQLLSTDYKFAVSFA 317

Query: 269 LMIIILFIRPQGLFKG 284
           +++++L  +P GLFKG
Sbjct: 318 ILVVVLLFKPTGLFKG 333


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: 263
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: 336
Length adjustment: 27
Effective length of query: 259
Effective length of database: 309
Effective search space:    80031
Effective search space used:    80031
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