GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araG in Herbaspirillum seropedicae SmR1

Align L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized)
to candidate HSERO_RS05320 HSERO_RS05320 ribonucleotide-diphosphate reductase subunit alpha

Query= CharProtDB::CH_014279
         (504 letters)



>FitnessBrowser__HerbieS:HSERO_RS05320
          Length = 502

 Score =  353 bits (905), Expect = e-101
 Identities = 195/493 (39%), Positives = 294/493 (59%), Gaps = 6/493 (1%)

Query: 8   LSFRGIGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGSVVIN 67
           L   GI K F  V  L  +  +  AG+VHAL+GENGAGKSTL+KIL G   P  G + I+
Sbjct: 2   LQLTGIKKNFGPVTVLRGVDLEVRAGEVHALLGENGAGKSTLMKILCGIVRPDAGEIRID 61

Query: 68  GQEMSFSDTTAALNAGVAIIYQELHLVPEMTVAENIYLG-QLPHKGGIVNRSLLNYEAGL 126
           GQ   F    AA+  GV +++QE  L+P +   +N++L  +L  + G + R+ +   A  
Sbjct: 62  GQPCRFDSYRAAIAGGVGVVFQEFSLIPYLDAVDNMFLARELRSRWGWLQRAAMRRRAQE 121

Query: 127 QLKHLGMDIDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDNLFRVI 186
            +  LG+ I  D P+  LS+ Q Q VEIAKALA +A+I+  DEPT++L+  E+++LF V+
Sbjct: 122 IIGQLGVAIPLDVPVCKLSVAQQQFVEIAKALALDARILVLDEPTATLTPAEVEHLFAVM 181

Query: 187 RELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHDALVQAMVGRDIG 246
           R LR +G  I+++SH +EEIF + D ITV +DG YV T    + VD   LV+ MVGR I 
Sbjct: 182 RSLRAQGVAIIFISHHLEEIFEICDRITVLRDGAYVATCATAE-VDQARLVEMMVGRRIE 240

Query: 247 DIYGWQPRSYGEER----LRLDAVKAPGVRTPISLAVRSGEIVGLFGLVGAGRSELMKGM 302
           + +  +P   GE      L + A++           +R GEI+G  GLVG+GR+E +  M
Sbjct: 241 NCFPPKPAKGGEGEGEVVLEVHALQLRRQAPVSQFQLRRGEILGFAGLVGSGRTETVLAM 300

Query: 303 FGGTQITAGQVYIDQQPIDIRKPSHAIAAGMMLCPEDRKAEGIIPVHSVRDNINISARRK 362
            G     + ++ +   P+    P+ A+ AG+ L PE RK +G+I   S+  N++++   K
Sbjct: 301 LGAHAALSCKLSMHGVPLRFADPAQALQAGIGLLPESRKEQGLITSFSILHNVSLNNYGK 360

Query: 363 HVLGGCVINNGWEENNADHHIRSLNIKTPGAEQLIMNLSGGNQQKAILGRWLSEEMKVIL 422
           + LGG  ++   E+   +  ++ + +K PGA+  +  LSGGNQQK ++ RW++  MKV++
Sbjct: 361 YRLGGLFLDRRREQQATEAAMQRVRVKAPGAQVRVDTLSGGNQQKVVIARWINHAMKVLI 420

Query: 423 LDEPTRGIDVGAKHEIYNVIYALAAQGVAVLFASSDLPEVLGVADRIVVMREGEIAGELL 482
            DEPTRGIDVGAK EIY ++    AQG ++L  SS+LPEV+G+ADR+ V R G I   L 
Sbjct: 421 FDEPTRGIDVGAKSEIYQLMREFTAQGYSILMISSELPEVVGMADRVCVFRGGGIVATLE 480

Query: 483 HEQADERQALSLA 495
            E  +  + ++ A
Sbjct: 481 GEAVNAEEIMTHA 493



 Score = 75.5 bits (184), Expect = 4e-18
 Identities = 57/227 (25%), Positives = 103/227 (45%), Gaps = 15/227 (6%)

Query: 28  FDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGSVVINGQEMSFSDTTAALNAGVAII 87
           F    G++    G  G+G++  +  + G +A  +  + ++G  + F+D   AL AG+ ++
Sbjct: 275 FQLRRGEILGFAGLVGSGRTETVLAMLGAHAALSCKLSMHGVPLRFADPAQALQAGIGLL 334

Query: 88  YQ---ELHLVPEMTVAENIYLGQLP--HKGGIV---NRSLLNYEAGLQ---LKHLGMDID 136
            +   E  L+   ++  N+ L        GG+     R     EA +Q   +K  G  + 
Sbjct: 335 PESRKEQGLITSFSILHNVSLNNYGKYRLGGLFLDRRREQQATEAAMQRVRVKAPGAQVR 394

Query: 137 PDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDNLFRVIRELRKEGRVI 196
            DT    LS G  Q V IA+ +    K++ FDEPT  +       +++++RE   +G  I
Sbjct: 395 VDT----LSGGNQQKVVIARWINHAMKVLIFDEPTRGIDVGAKSEIYQLMREFTAQGYSI 450

Query: 197 LYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHDALVQAMVGR 243
           L +S  + E+  ++D + VF+ G  V T         + +  A  GR
Sbjct: 451 LMISSELPEVVGMADRVCVFRGGGIVATLEGEAVNAEEIMTHATTGR 497


Lambda     K      H
   0.319    0.136    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: 670
Number of extensions: 40
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: 504
Length of database: 502
Length adjustment: 34
Effective length of query: 470
Effective length of database: 468
Effective search space:   219960
Effective search space used:   219960
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 (21.7 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