Alignments for a candidate for H281DRAFT_01113 in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Alignments for a candidate for H281DRAFT_01113 in Pseudomonas putida KT2440

Align deoxynucleoside transporter, ATPase component (characterized)
to candidate PP_2455 PP_2455 ribose ABC transporter - ATP-binding subunit

Query= reanno::Burk376:H281DRAFT_01113
         (515 letters)



>FitnessBrowser__Putida:PP_2455
          Length = 524

 Score =  287 bits (735), Expect = 6e-82
 Identities = 172/479 (35%), Positives = 271/479 (56%), Gaps = 12/479 (2%)

Query: 34  VSLSFQRGQIYHLLGENGCGKSTLIKIISGAQPPDEGQLVIEGVPHARLSALEALAAGIE 93
           VSLS + G++  L GENG GKSTL K+ISG + P  G +   G  +A  S  EA   G+ 
Sbjct: 34  VSLSLRAGEVLALTGENGAGKSTLSKLISGLEVPTTGHMTYRGQAYAPGSRGEAERLGVR 93

Query: 94  TVYQDLSLLPNMSVAENVALTSELATHEGRLARTFDRRVLAATAARA-LEAVGLPGNSEF 152
            V Q+L+LLP ++VAEN+ L + L +  G ++    R++  A  AR  L+A+        
Sbjct: 94  MVMQELNLLPTLTVAENLFLDN-LPSRFGWISHKRLRQLATAAMARVGLDAID------- 145

Query: 153 QSTLIEQLPLATRQLVAIARAIASEAKFVIMDEPTTSLTQKEVDNLIAVLANLRAQGVTV 212
             T + +L +  +Q+V IAR +  +   +I+DEPT  LT +EV  L   +  LRA+GV +
Sbjct: 146 PDTPVGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREVALLFTQIERLRARGVAI 205

Query: 213 LFVSHKLDECYAIGGEVIVLRDGQKMAQGPIAEFTKAQISELMTGRHLSNERYRESAHAQ 272
           +++SH+L+E   +   ++VLRDG+ +   PI  ++ A++  LM GR L            
Sbjct: 206 VYISHRLEELQRVAQRIVVLRDGKLVCDEPIQRYSSAELVNLMVGRELGEHIDLGRRQLG 265

Query: 273 DIVLDVRGFTRAGQFSDVSFKLHGGEILGVTGLLDSGRNELARALAGVAPAQSGDVLLDG 332
             +L V    R  +  +VSF++  GEI G++GL+ +GR EL R + G   A SG + L  
Sbjct: 266 APLLKVDKLCRGDKVREVSFEVRAGEIFGISGLIGAGRTELLRLIYGADRADSGGIALGQ 325

Query: 333 --QQIALRTPSDAKRHRIGYVPEDRLNEGLFLDKPIRDNVITAMISSLRDRFGQIDRTRA 390
             Q +++ +P  A R  I  + EDR  EGL L + I  N+    + ++  R G +D    
Sbjct: 326 PPQAVSIDSPKAAVRAGIALITEDRKGEGLLLTQSISANIALGNLGAV-SRAGVLDSEAE 384

Query: 391 QALAEQTVKELQIATPGVDKPVQSLSGGNQQRVLIGRWLAIDPRVLILHGPTVGVDVGSK 450
           +ALAE+ ++ ++I + G  + V  LSGGNQQ+V+IGRWL  D +VL+   PT G+DVG+K
Sbjct: 385 KALAERQIQAMRIRSAGAQQVVGELSGGNQQKVVIGRWLERDCQVLLFDEPTRGIDVGAK 444

Query: 451 DIIYRIMQRLSQRGIGIILISDDLPELLQNCDRILMMKKGHVSAEYRADELSEADLYHA 509
             IY ++  L+++G  ++++S DL EL+  CDRI ++  G +   +  D  S+  L  A
Sbjct: 445 FDIYGLLAELARQGKALVVVSSDLRELMLICDRIAVLSAGRLIDTFARDHWSQDQLLAA 503



 Score = 89.7 bits (221), Expect = 2e-22
 Identities = 70/253 (27%), Positives = 117/253 (46%), Gaps = 23/253 (9%)

Query: 269 AHAQDIVLDVRGFTRAGQ---FSDVSFKLHGGEILGVTGLLDSGRNELARALAGVAPAQS 325
           A A ++VL   G  +        +VS  L  GE+L +TG   +G++ L++ ++G+    +
Sbjct: 10  ALANEVVLAASGLGKTYAQPVLGEVSLSLRAGEVLALTGENGAGKSTLSKLISGLEVPTT 69

Query: 326 GDVLLDGQQIALRTPSDAKR-------HRIGYVPEDRLNEGLFLDKPIRDNVITAMISSL 378
           G +   GQ  A  +  +A+R         +  +P   + E LFLD             +L
Sbjct: 70  GHMTYRGQAYAPGSRGEAERLGVRMVMQELNLLPTLTVAENLFLD-------------NL 116

Query: 379 RDRFGQIDRTRAQALAEQTVKELQIATPGVDKPVQSLSGGNQQRVLIGRWLAIDPRVLIL 438
             RFG I   R + LA   +  + +     D PV  L  G+QQ V I R L  D  VLIL
Sbjct: 117 PSRFGWISHKRLRQLATAAMARVGLDAIDPDTPVGELGIGHQQMVEIARNLIGDCHVLIL 176

Query: 439 HGPTVGVDVGSKDIIYRIMQRLSQRGIGIILISDDLPELLQNCDRILMMKKGHVSAEYRA 498
             PT  +      +++  ++RL  RG+ I+ IS  L EL +   RI++++ G +  +   
Sbjct: 177 DEPTAMLTAREVALLFTQIERLRARGVAIVYISHRLEELQRVAQRIVVLRDGKLVCDEPI 236

Query: 499 DELSEADLYHALL 511
              S A+L + ++
Sbjct: 237 QRYSSAELVNLMV 249



 Score = 68.6 bits (166), Expect = 5e-16
 Identities = 58/211 (27%), Positives = 98/211 (46%), Gaps = 10/211 (4%)

Query: 31  LRGVSLSFQRGQIYHLLGENGCGKSTLIKIISGAQPPDEGQLVIEGVPHARL--SALEAL 88
           +R VS   + G+I+ + G  G G++ L+++I GA   D G + +   P A    S   A+
Sbjct: 280 VREVSFEVRAGEIFGISGLIGAGRTELLRLIYGADRADSGGIALGQPPQAVSIDSPKAAV 339

Query: 89  AAGIETVYQDL---SLLPNMSVAENVALTSELATHEGRLARTFDRRVLAATAARALEAVG 145
            AGI  + +D     LL   S++ N+AL +  A      A   D     A A R ++A+ 
Sbjct: 340 RAGIALITEDRKGEGLLLTQSISANIALGNLGAVSR---AGVLDSEAEKALAERQIQAMR 396

Query: 146 LPGNSEFQSTLIEQLPLATRQLVAIARAIASEAKFVIMDEPTTSLTQKEVDNLIAVLANL 205
           +   S     ++ +L    +Q V I R +  + + ++ DEPT  +      ++  +LA L
Sbjct: 397 I--RSAGAQQVVGELSGGNQQKVVIGRWLERDCQVLLFDEPTRGIDVGAKFDIYGLLAEL 454

Query: 206 RAQGVTVLFVSHKLDECYAIGGEVIVLRDGQ 236
             QG  ++ VS  L E   I   + VL  G+
Sbjct: 455 ARQGKALVVVSSDLRELMLICDRIAVLSAGR 485


Lambda     K      H
   0.319    0.135    0.376 

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: 36
Number of successful extensions: 9
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: 515
Length of database: 524
Length adjustment: 35
Effective length of query: 480
Effective length of database: 489
Effective search space:   234720
Effective search space used:   234720
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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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