Alignments for a candidate for nupA in Stutzerimonas stutzeri A1501

GapMind for catabolism of small carbon sources

Alignments for a candidate for nupA in Stutzerimonas stutzeri A1501

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 WP_011914604.1 PST_RS17845 ABC transporter ATP-binding protein

Query= TCDB::Q8DU37
         (510 letters)



>NCBI__GCF_000013785.1:WP_011914604.1
          Length = 525

 Score =  341 bits (874), Expect = 4e-98
 Identities = 200/486 (41%), Positives = 284/486 (58%), Gaps = 10/486 (2%)

Query: 4   HVIEMREITKKFDDFVANDHINLDLRKGEIHALLGENGAGKSTLMNMLAGLLEPTSGSIK 63
           + I++  ++K FD F+A    +   R GE+HALLGENGAGKS+LMN+ AGL  P SGS+ 
Sbjct: 5   NAIQLSGVSKSFDGFMALSQADFTARWGEVHALLGENGAGKSSLMNIAAGLYAPESGSLL 64

Query: 64  INGSAVTIDSPSKSAQLGIGMVHQHFMLVEAFTVTENIIL------GNEVVKNGILD-LK 116
           IN +AV +  P  +++  IGMVHQHF LV+ FTV ENI L      GN          L 
Sbjct: 65  INDNAVRLSGPRDASRYHIGMVHQHFKLVKPFTVAENIQLALPEGPGNHAFSGSHRQRLA 124

Query: 117 KAGQEIKALSEKYGLAVDPNAKIADISVGAQQRVEILKTLYRGADILIFDEPTAVLTPSE 176
              Q I   + + G ++DP      +SV  QQRVEILK L  GA ILI DEPTAVLT  E
Sbjct: 125 ALEQRISDKAAELGFSIDPRKITESLSVAEQQRVEILKVLLAGARILILDEPTAVLTDGE 184

Query: 177 IQELMTIMKSLVKEGKSIILITHKLDEIRSVADRVTVIRRGKSIETVEVSGTTSQDLAEM 236
            + L+  +++  ++G ++IL+THK+ +++  ADRVTV+R G++I+T++    +  +L  +
Sbjct: 185 AERLLETVRAFARQGAAVILVTHKMSDVKRFADRVTVMRGGRTIQTLDPQTVSVPELVRL 244

Query: 237 MVGRSVSFTIEKTPTKPKETILSIKDLVVNENRGIPAIKGLSLEVKAGEIIGIAGIDGNG 296
            VG S   + E  P  P E  L ++DL      G   + G++L ++AGEI GIAG+ GNG
Sbjct: 245 TVGESAPAS-EYQPAIPGEVRLQVRDLRSTGAGGQGVLNGVNLSLRAGEIYGIAGVGGNG 303

Query: 297 QSELVQAITGLRKIKSGHLTIKG-QDVTKLSTRKITELSVGHVPEDRHRDGLILELTMAE 355
           QSEL   + GL +   G L + G  D+ + S  +  EL +  +P DR+   L  EL++AE
Sbjct: 304 QSELANVLMGLPEPCDGTLELTGFGDLRRASAEQRRELRIAAIPADRYGAALAGELSVAE 363

Query: 356 NLALQTYYKAPLSHNGVLNYSKINEHGRHLMQEFDVRGANEL-IPAKGFSGGNQQKAIIA 414
           N  +   +         L   ++       +  FDV+G   L   A   SGGN QK +IA
Sbjct: 364 NFGVGQVHSGRYGSFFRLRRKRLEAEAAEAVAGFDVQGVRSLKQKAALLSGGNAQKLVIA 423

Query: 415 REVDRDPDLLIVSQPTRGLDVGAIEYIHKRLIAERDEGKAVLLVSFELDEILNLSDRIAV 474
           RE  RDP L++V  P+RGLDV A   +H RL A R+ G AVL++S +LDE+L L+DRI V
Sbjct: 424 REFSRDPLLVLVHSPSRGLDVRATAAVHARLRAAREAGAAVLVISEDLDEVLALADRIGV 483

Query: 475 IHDGQI 480
           +  G+I
Sbjct: 484 MSGGRI 489



 Score = 64.3 bits (155), Expect = 1e-14
 Identities = 61/246 (24%), Positives = 106/246 (43%), Gaps = 17/246 (6%)

Query: 270 GIPAIKGLSLEVKAGEIIGIAGIDGNGQSELVQAITGLRKIKSGHLTIKGQDVTKLSTRK 329
           G  A+       + GE+  + G +G G+S L+    GL   +SG L I    V     R 
Sbjct: 18  GFMALSQADFTARWGEVHALLGENGAGKSSLMNIAAGLYAPESGSLLINDNAVRLSGPRD 77

Query: 330 ITELSVGHVPEDRHRDGLILELTMAENLALQTYYKAPLSHNGVLNY--------SKINEH 381
            +   +G V +      L+   T+AEN+ L    + P +H    ++         +I++ 
Sbjct: 78  ASRYHIGMVHQHFK---LVKPFTVAENIQL-ALPEGPGNHAFSGSHRQRLAALEQRISDK 133

Query: 382 GRHLMQEFDVRGANELIPAKGFSGGNQQKAIIAREVDRDPDLLIVSQPTRGLDVGAIEYI 441
              L    D R   E +     S   QQ+  I + +     +LI+ +PT  L  G  E +
Sbjct: 134 AAELGFSIDPRKITESL-----SVAEQQRVEILKVLLAGARILILDEPTAVLTDGEAERL 188

Query: 442 HKRLIAERDEGKAVLLVSFELDEILNLSDRIAVIHDGQIQGIVTPETTNKQELGILMAGG 501
            + + A   +G AV+LV+ ++ ++   +DR+ V+  G+    + P+T +  EL  L  G 
Sbjct: 189 LETVRAFARQGAAVILVTHKMSDVKRFADRVTVMRGGRTIQTLDPQTVSVPELVRLTVGE 248

Query: 502 SIEREE 507
           S    E
Sbjct: 249 SAPASE 254



 Score = 63.5 bits (153), Expect = 2e-14
 Identities = 54/209 (25%), Positives = 98/209 (46%), Gaps = 14/209 (6%)

Query: 24  INLDLRKGEIHALLGENGAGKSTLMNMLAGLLEPTSGSIKINGSA-VTIDSPSKSAQLGI 82
           +NL LR GEI+ + G  G G+S L N+L GL EP  G++++ G   +   S  +  +L I
Sbjct: 284 VNLSLRAGEIYGIAGVGGNGQSELANVLMGLPEPCDGTLELTGFGDLRRASAEQRRELRI 343

Query: 83  GMV---HQHFMLVEAFTVTENIILGNEVVKNG----ILDLKKAGQEIKALSEKYGLAVDP 135
             +        L    +V EN  +G   V +G       L++   E +A     G  V  
Sbjct: 344 AAIPADRYGAALAGELSVAENFGVGQ--VHSGRYGSFFRLRRKRLEAEAAEAVAGFDVQG 401

Query: 136 ----NAKIADISVGAQQRVEILKTLYRGADILIFDEPTAVLTPSEIQELMTIMKSLVKEG 191
                 K A +S G  Q++ I +   R   +++   P+  L       +   +++  + G
Sbjct: 402 VRSLKQKAALLSGGNAQKLVIAREFSRDPLLVLVHSPSRGLDVRATAAVHARLRAAREAG 461

Query: 192 KSIILITHKLDEIRSVADRVTVIRRGKSI 220
            ++++I+  LDE+ ++ADR+ V+  G+ +
Sbjct: 462 AAVLVISEDLDEVLALADRIGVMSGGRIV 490


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: 612
Number of extensions: 23
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 510
Length of database: 525
Length adjustment: 35
Effective length of query: 475
Effective length of database: 490
Effective search space:   232750
Effective search space used:   232750
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 Apr 09 2024. The underlying query database was built on Sep 17 2021.

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Rules (tab-delimited)
Protein sequences (fasta format)
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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 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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