GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__HerbieS:HSERO_RS05320 HSERO_RS05320
           ribonucleotide-diphosphate reductase subunit alpha
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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