Alignments for a candidate for araVsh in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Alignments for a candidate for araVsh in Pseudomonas putida KT2440

Align ABC transporter related (characterized, see rationale)
to candidate PP_2455 PP_2455 ribose ABC transporter - ATP-binding subunit

Query= uniprot:A0KWY5
         (499 letters)



>FitnessBrowser__Putida:PP_2455
          Length = 524

 Score =  296 bits (758), Expect = 1e-84
 Identities = 177/474 (37%), Positives = 281/474 (59%), Gaps = 10/474 (2%)

Query: 3   LILELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDIL 62
           ++L    + K Y     L +VSL L AGEV AL GENGAGKSTL K+++G +    G + 
Sbjct: 15  VVLAASGLGKTY-AQPVLGEVSLSLRAGEVLALTGENGAGKSTLSKLISGLEVPTTGHMT 73

Query: 63  FLGEPQHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNLFLGYEPRRLGLIHFKKMYADAR 122
           + G+     +  +A++ G+  V QE+NL+P LTVA+NLFL   P R G I  K++   A 
Sbjct: 74  YRGQAYAPGSRGEAERLGVRMVMQELNLLPTLTVAENLFLDNLPSRFGWISHKRLRQLAT 133

Query: 123 AVLTQFKLD-IDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFG 181
           A + +  LD ID   P+ +  I  QQ++ IAR +     VL+LDEPTA L A+EV +LF 
Sbjct: 134 AAMARVGLDAIDPDTPVGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREVALLFT 193

Query: 182 ILNQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLGRSL 241
            + +L+A+GVAIV+I+H L+++ +++ RI VLR+G+ + +         +L+  M+GR L
Sbjct: 194 QIERLRARGVAIVYISHRLEELQRVAQRIVVLRDGKLVCDEPIQRYSSAELVNLMVGREL 253

Query: 242 QEQLVDKQEKERTVTRAEAVLLSLEDVSVKGSIQSMNLTVPKGQAVGLAGLLGSGRSEVC 301
            E  +D   ++       A LL ++ +     ++ ++  V  G+  G++GL+G+GR+E+ 
Sbjct: 254 GEH-IDLGRRQ-----LGAPLLKVDKLCRGDKVREVSFEVRAGEIFGISGLIGAGRTELL 307

Query: 302 NAVFGLDLVDSGSIHLAG--QKLNLSQPVDAISAGIALCPEDRKIDGIIGPLSIRENIIL 359
             ++G D  DSG I L    Q +++  P  A+ AGIAL  EDRK +G++   SI  NI L
Sbjct: 308 RLIYGADRADSGGIALGQPPQAVSIDSPKAAVRAGIALITEDRKGEGLLLTQSISANIAL 367

Query: 360 ALQARIGWWRYLSNTRQQEIAQFFIDKLQIATPDADKPIEQLSGGNQQKVILARWLAIEP 419
                +     L +  ++ +A+  I  ++I +  A + + +LSGGNQQKV++ RWL  + 
Sbjct: 368 GNLGAVSRAGVLDSEAEKALAERQIQAMRIRSAGAQQVVGELSGGNQQKVVIGRWLERDC 427

Query: 420 ILLVLDEPTRGIDIGAHAEIVKLIRTLCDEGMSLLVASSELDELVAFSNKVVVL 473
            +L+ DEPTRGID+GA  +I  L+  L  +G +L+V SS+L EL+   +++ VL
Sbjct: 428 QVLLFDEPTRGIDVGAKFDIYGLLAELARQGKALVVVSSDLRELMLICDRIAVL 481



 Score = 81.3 bits (199), Expect = 8e-20
 Identities = 62/228 (27%), Positives = 117/228 (51%), Gaps = 12/228 (5%)

Query: 277 MNLTVPKGQAVGLAGLLGSGRSEVCNAVFGLDLVDSGSIHLAGQKLNLSQPVDAISAGIA 336
           ++L++  G+ + L G  G+G+S +   + GL++  +G +   GQ        +A   G+ 
Sbjct: 34  VSLSLRAGEVLALTGENGAGKSTLSKLISGLEVPTTGHMTYRGQAYAPGSRGEAERLGVR 93

Query: 337 LCPEDRKIDGIIGPLSIRENIILA-LQARIGWWRYLSNTRQQEIAQFFIDKLQIATPDAD 395
           +  ++  +   +  L++ EN+ L  L +R GW   +S+ R +++A   + ++ +   D D
Sbjct: 94  MVMQELNL---LPTLTVAENLFLDNLPSRFGW---ISHKRLRQLATAAMARVGLDAIDPD 147

Query: 396 KPIEQLSGGNQQKVILARWLAIEPILLVLDEPTRGIDIGAHAEIVKLIRTLCDEGMSLLV 455
            P+ +L  G+QQ V +AR L  +  +L+LDEPT  +     A +   I  L   G++++ 
Sbjct: 148 TPVGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREVALLFTQIERLRARGVAIVY 207

Query: 456 ASSELDELVAFSNKVVVLRDRYAV-----RELSGAELTSQHVMQAIAE 498
            S  L+EL   + ++VVLRD   V     +  S AEL +  V + + E
Sbjct: 208 ISHRLEELQRVAQRIVVLRDGKLVCDEPIQRYSSAELVNLMVGRELGE 255



 Score = 79.3 bits (194), Expect = 3e-19
 Identities = 61/225 (27%), Positives = 112/225 (49%), Gaps = 10/225 (4%)

Query: 20  LEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILFLGEPQH---FNTPMDA 76
           + +VS  + AGE+  + G  GAG++ L++++ GA   D G I  LG+P      ++P  A
Sbjct: 280 VREVSFEVRAGEIFGISGLIGAGRTELLRLIYGADRADSGGIA-LGQPPQAVSIDSPKAA 338

Query: 77  QKAGISTVYQE---VNLVPNLTVAQNLFLGY--EPRRLGLIHFKKMYADARAVLTQFKL- 130
            +AGI+ + ++     L+   +++ N+ LG      R G++  +   A A   +   ++ 
Sbjct: 339 VRAGIALITEDRKGEGLLLTQSISANIALGNLGAVSRAGVLDSEAEKALAERQIQAMRIR 398

Query: 131 DIDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFGILNQLKAKG 190
                  + + S   QQ + I R +    +VL+ DEPT  +D      ++G+L +L  +G
Sbjct: 399 SAGAQQVVGELSGGNQQKVVIGRWLERDCQVLLFDEPTRGIDVGAKFDIYGLLAELARQG 458

Query: 191 VAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEA 235
            A+V ++  L ++  I DRI VL  G+ I  +      Q +L+ A
Sbjct: 459 KALVVVSSDLRELMLICDRIAVLSAGRLIDTFARDHWSQDQLLAA 503


Lambda     K      H
   0.319    0.136    0.377 

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: 610
Number of extensions: 32
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: 499
Length of database: 524
Length adjustment: 35
Effective length of query: 464
Effective length of database: 489
Effective search space:   226896
Effective search space used:   226896
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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Steps (tab-delimited)
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 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