Alignments for a candidate for nupA in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for nupA in Herbaspirillum seropedicae SmR1

Align RnsB, component of The (deoxy)ribonucleoside permease; probably takes up all deoxy- and ribonucleosides (cytidine, uridine, adenosine and toxic analogues, fluorocytidine and fluorouridine tested), but not ribose or nucleobases (characterized)
to candidate HSERO_RS21310 HSERO_RS21310 ABC transporter

Query= TCDB::Q8DU37
         (510 letters)



>FitnessBrowser__HerbieS:HSERO_RS21310
          Length = 518

 Score =  338 bits (867), Expect = 3e-97
 Identities = 195/504 (38%), Positives = 298/504 (59%), Gaps = 19/504 (3%)

Query: 6   IEMREITKKFDDFVANDHINLDLRKGEIHALLGENGAGKSTLMNMLAGLLEPTSGSIKIN 65
           +E+  + K +   +AND ++L +  GEIHA+LGENGAGKSTLM ++ G ++P +G I+ N
Sbjct: 8   LEISHVRKAYPGVLANDDVSLAVAPGEIHAVLGENGAGKSTLMKIIFGAVKPDAGEIRWN 67

Query: 66  GSAVTIDSPSKSAQLGIGMVHQHFMLVEAFTVTENIILGNEVVKNGILDLKKAGQEIKAL 125
           G AV I +P  + +LGI MV QHF L +  TVTENI LG +       DLK+  + I   
Sbjct: 68  GEAVQIANPQVARKLGIAMVFQHFSLFDTLTVTENIALGLDAKT----DLKELAERITRT 123

Query: 126 SEKYGLAVDPNAKIADISVGAQQRVEILKTLYRGADILIFDEPTAVLTPSEIQELMTIMK 185
            EKYGL ++P   +  +SVG +QRVEI++ L     +LI DEPT+VLTP  +++L   ++
Sbjct: 124 GEKYGLELEPQRHVHTLSVGERQRVEIVRALLTEPQLLILDEPTSVLTPQAVEKLFVTLR 183

Query: 186 SLVKEGKSIILITHKLDEIRSVADRVTVIRRGKSIETVEVSGTTSQDLAEMMVGRS-VSF 244
            L  EG SI+ I+HKLDEIR++    TV+R G+     +    +S  L+ MM+G   V  
Sbjct: 184 RLADEGCSILYISHKLDEIRALCHSATVMRGGRVTGNCDPRNESSASLSRMMIGDELVRL 243

Query: 245 TIEKTPTKPKETILSIKDLVVNENRGIPA-------IKGLSLEVKAGEIIGIAGIDGNGQ 297
             E+ P    E++ + + L VN    +P        +K +  EV+AGEI+GIAG+ GNGQ
Sbjct: 244 QRERNP----ESMRNERKLHVNR-LSLPKAHLFATELKDIECEVRAGEIVGIAGVSGNGQ 298

Query: 298 SELVQAITGLRKIKSGHLTIKGQD-VTKLSTRKITELSVGHVPEDRHRDGLILELTMAEN 356
            EL+ A++G  +  + H+ + G   V  LS        +G VPE+R   G +  L++  N
Sbjct: 299 QELLAALSGEDQRAAPHMIMLGSKAVGDLSPNPRRAAGLGLVPEERLGRGAVPTLSLTAN 358

Query: 357 LALQTYYKAPLSHNGVLNYSKINEHGRHLMQEFDVRGANELIPAKGFSGGNQQKAIIARE 416
           + L ++ KAP    G++++         +++ F V+ A    PAK  SGGN QK I+ RE
Sbjct: 359 MLL-SHQKAPYVKRGMIDFGFTRRAAASIIERFKVKAAGPDAPAKSLSGGNLQKFIVGRE 417

Query: 417 VDRDPDLLIVSQPTRGLDVGAIEYIHKRLIAERDEGKAVLLVSFELDEILNLSDRIAVIH 476
           ++R P + +V+QPT G+DVGA   IH  ++  + EG AVL++S ELDE+  L DR+ VI 
Sbjct: 418 MERKPAVFVVAQPTWGVDVGAAAQIHGEILKLKQEGCAVLVISEELDELFALCDRLHVIA 477

Query: 477 DGQIQGIVTPETTNKQELGILMAG 500
            G++   +  E   ++++G+ M+G
Sbjct: 478 KGRLSPSIPIEQATREQVGVWMSG 501



 Score = 76.3 bits (186), Expect = 3e-18
 Identities = 66/236 (27%), Positives = 104/236 (44%), Gaps = 12/236 (5%)

Query: 270 GIPAIKGLSLEVKAGEIIGIAGIDGNGQSELVQAITGLRKIKSGHLTIKGQDVTKLSTRK 329
           G+ A   +SL V  GEI  + G +G G+S L++ I G  K  +G +   G+ V   + + 
Sbjct: 19  GVLANDDVSLAVAPGEIHAVLGENGAGKSTLMKIIFGAVKPDAGEIRWNGEAVQIANPQV 78

Query: 330 ITELSVGHVPEDRHRDGLILELTMAENLALQTYYKAPLSHNGVLNYSKINEHGRHLMQEF 389
             +L +  V +      L   LT+ EN+AL    K  L            ++G  L  + 
Sbjct: 79  ARKLGIAMVFQ---HFSLFDTLTVTENIALGLDAKTDLKELAERITRTGEKYGLELEPQR 135

Query: 390 DVRGANELIPAKGFSGGNQQKAIIAREVDRDPDLLIVSQPTRGLDVGAIEYIHKRLIAER 449
            V            S G +Q+  I R +  +P LLI+ +PT  L   A+E +   L    
Sbjct: 136 HVHT---------LSVGERQRVEIVRALLTEPQLLILDEPTSVLTPQAVEKLFVTLRRLA 186

Query: 450 DEGKAVLLVSFELDEILNLSDRIAVIHDGQIQGIVTPETTNKQELGILMAGGSIER 505
           DEG ++L +S +LDEI  L     V+  G++ G   P   +   L  +M G  + R
Sbjct: 187 DEGCSILYISHKLDEIRALCHSATVMRGGRVTGNCDPRNESSASLSRMMIGDELVR 242


Lambda     K      H
   0.315    0.135    0.363 

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: 543
Number of extensions: 26
Number of successful extensions: 6
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: 510
Length of database: 518
Length adjustment: 35
Effective length of query: 475
Effective length of database: 483
Effective search space:   229425
Effective search space used:   229425
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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

GapMind for catabolism of small carbon sources