GapMind for catabolism of small carbon sources

 

Alignments for a candidate for BPHYT_RS16930 in Herbaspirillum seropedicae SmR1

Align Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale)
to candidate HSERO_RS03640 HSERO_RS03640 D-ribose transporter ATP-binding protein

Query= uniprot:A0A165ZSX8
         (514 letters)



>FitnessBrowser__HerbieS:HSERO_RS03640
          Length = 502

 Score =  383 bits (984), Expect = e-111
 Identities = 207/494 (41%), Positives = 309/494 (62%), Gaps = 9/494 (1%)

Query: 16  LRFNGIGKSFPGVQALANISFVAHPGQVHALMGENGAGKSTLLKILGGAYIPSSGDLQIG 75
           L+  GI KSF    AL+++     PG++HALMGENGAGKSTL+K+L G + P  G++ + 
Sbjct: 11  LQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILLD 70

Query: 76  EQTMAFKGTADSIASGVAVIHQELHLVPEMTVAENLFLG-HLPARFGLVNRGVLRQQALT 134
            + +A +    S A+G+ +I+QEL + P ++VA N+F+G  L  R GL++   +R +   
Sbjct: 71  GRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAAMRSRTDA 130

Query: 135 LLKGLADEIDPQEKVGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRLMAII 194
           +L+ L       +  GRLS+ ++Q VEIA+AL   + ++  DEPT++LS RE ++L  ++
Sbjct: 131 VLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFNVV 190

Query: 195 GRLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRYVRTFENMSELTHDQLVTCMVGRDIQ 254
            RLRDEG  ++Y+SHRM EV+ + + VTV +DG +V       E+  +++V  MVGR + 
Sbjct: 191 RRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVR-DEIDSERIVQMMVGRSLS 249

Query: 255 DIYDYRPRERGDVA-----LQVKGLLGPGLHEPVSFQVHKGEILGLFGLVGAGRTELLRL 309
           + Y ++     D A     +QV+ L G G   P SF V  GE+LG  GLVGAGRTEL RL
Sbjct: 250 EFYQHQRIAPADAAQLPTVMQVRALAG-GKIRPASFDVRAGEVLGFAGLVGAGRTELARL 308

Query: 310 LSGLERQREGSLVLHDKELKLRSPRDAIAAGVLLCPEDRKKEGIIPLGSVGENINISARP 369
           L G + +  G ++L  + + +  PR A+ AG+   PEDRK +G+    +V  N  ++   
Sbjct: 309 LFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAANATMNVAS 368

Query: 370 SHSTLGCLLRGDWERGNADKQIKSLKVKTPTAGQKIMYLSGGNQQKAILGRWLSMPMKVL 429
            H+ LG L+R     G A   I+ L VK       +  LSGGNQQK +L RWL +  KVL
Sbjct: 369 RHTRLG-LVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWLEIAPKVL 427

Query: 430 LLDEPTRGIDIGAKAEIYQIIHNLAADGIAVIVVSSDLMEVMGISDRILVLCEGAMRGEL 489
           +LDEPTRG+DI AK+EIYQ++H LA+ G+AV+V+SS+L EV+GI DR+LV+ EG + GEL
Sbjct: 428 ILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVMREGMITGEL 487

Query: 490 SRDQANESNLLQLA 503
           +     + N+++LA
Sbjct: 488 AGAAITQENIMRLA 501



 Score = 91.3 bits (225), Expect = 7e-23
 Identities = 66/237 (27%), Positives = 122/237 (51%), Gaps = 20/237 (8%)

Query: 287 VHKGEILGLFGLVGAGRTELLRLLSGLERQREGSLVLHDKELKLRSPRDAIAAGVLLCPE 346
           +  GEI  L G  GAG++ L+++LSG+    +G ++L  + + LR P  + AAG+ L  +
Sbjct: 33  IRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILLDGRPVALRDPGASRAAGINLIYQ 92

Query: 347 DRKKEGIIPLGSVGENINISARPSHSTLGCLLRGDWERGNADKQIKSLKV---KTPTAGQ 403
           +     + P  SV  N+ + +    + LG L+     R   D  ++ L      +  AG+
Sbjct: 93  EL---AVAPNISVAANVFMGSE-LRTRLG-LIDHAAMRSRTDAVLRQLGAGFGASDLAGR 147

Query: 404 KIMYLSGGNQQKAILGRWLSMPMKVLLLDEPTRGIDIGAKAEIYQIIHNLAADGIAVIVV 463
               LS   QQ+  + R L    +++++DEPT  +      +++ ++  L  +G+A+I +
Sbjct: 148 ----LSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFNVVRRLRDEGLAIIYI 203

Query: 464 SSDLMEVMGISDRILVLCEGAMRGELSRDQANESNLLQLALPR--------QRVADA 512
           S  + EV  ++DR+ VL +G+  GEL RD+ +   ++Q+ + R        QR+A A
Sbjct: 204 SHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVGRSLSEFYQHQRIAPA 260


Lambda     K      H
   0.320    0.138    0.391 

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: 650
Number of extensions: 32
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 514
Length of database: 502
Length adjustment: 34
Effective length of query: 480
Effective length of database: 468
Effective search space:   224640
Effective search space used:   224640
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (24.6 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