Alignments for a candidate for H281DRAFT_01113 in Pseudomonas stutzeri RCH2

GapMind for catabolism of small carbon sources

Alignments for a candidate for H281DRAFT_01113 in Pseudomonas stutzeri RCH2

Align deoxynucleoside transporter, ATPase component (characterized)
to candidate GFF1357 Psest_1392 ABC-type uncharacterized transport systems, ATPase components

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



>FitnessBrowser__psRCH2:GFF1357
          Length = 518

 Score =  250 bits (639), Expect = 8e-71
 Identities = 164/490 (33%), Positives = 252/490 (51%), Gaps = 21/490 (4%)

Query: 16  LEVVGVHKRFTGVHALRGVSLSFQRGQIYHLLGENGCGKSTLIKIISGAQPPDEGQLVIE 75
           L++ G+ K++ G  A   + LS Q G+I+ LLGENG GKSTL+KII G   PD G++  +
Sbjct: 9   LQLCGITKQYPGCLANDRIDLSIQPGEIHALLGENGAGKSTLMKIIYGVTQPDAGEIHWQ 68

Query: 76  GVPHARLSALEALAAGIETVYQDLSLLPNMSVAENVALTSELATHEGRLARTFDRRVLAA 135
           G         +A   GI  V+Q  SL   +SVAEN+AL           A+    + L  
Sbjct: 69  GERVTMRDPAQARERGIGMVFQHFSLFETLSVAENIALALG--------AKAGTPKQLEP 120

Query: 136 TAARALEAVGLPGNSEFQSTLIEQLPLATRQLVAIARAIASEAKFVIMDEPTTSLTQKEV 195
                 +  G+P   +    L+  L +  RQ V I R +  + + +I+DEPT+ LT +E 
Sbjct: 121 KIREVSQRYGMPLEPQ---RLVHSLSIGERQRVEIIRCLMQDIRLLILDEPTSVLTPQEA 177

Query: 196 DNLIAVLANLRAQGVTVLFVSHKLDECYAIGGEVIVLRDGQKMAQGPIAEFTKAQISELM 255
           D L   L  L A+G ++LF+SHKL+E  A+     VLR G+   +   AE +  +++ LM
Sbjct: 178 DELFVTLRRLAAEGCSILFISHKLNEVRALCQSATVLRAGRVSGECIPAECSDLELARLM 237

Query: 256 TG--RHLSNERYRESAHAQDIVLDVRGFTRAGQFS----DVSFKLHGGEILGVTGLLDSG 309
            G    L  E  +    A  + ++   +  A  F     +V  ++  GEI+G+ G+  +G
Sbjct: 238 VGDAEGLEAEYPKSEGRAPFLRVERLSWHNADPFGVSLKEVDLEVRAGEIVGIAGVAGNG 297

Query: 310 RNELARALAG---VAPAQSGDVLLDGQQIALRTPSDAKRHRIGYVPEDRLNEGLFLDKPI 366
           ++EL   L+G   +  AQ+  +   G  +A   P   +RH + +VP +RL  G      +
Sbjct: 298 QDELLALLSGEQRLQAAQAMRIRFLGDDVAHLRPGARRRHGMAFVPAERLGHGAVPSMSL 357

Query: 367 RDN-VITAMISSLRDRFGQIDRTRAQALAEQTVKELQIATPGVDKPVQSLSGGNQQRVLI 425
            DN ++TA   +     G I R R +A AEQ ++   + TP    P  SLSGGN Q+ ++
Sbjct: 358 ADNGLLTAYQQTGMVEQGLIRRGRVRAFAEQVIQRFAVKTPDAQTPAASLSGGNLQKFIL 417

Query: 426 GRWLAIDPRVLILHGPTVGVDVGSKDIIYRIMQRLSQRGIGIILISDDLPELLQNCDRIL 485
           GR +   P++LI   PT GVDVG+   I+R +  L   G  I++IS+DL EL Q  DRI 
Sbjct: 418 GREILQQPKLLIAAHPTWGVDVGAAAAIHRALIELRDAGAAILVISEDLEELFQISDRIA 477

Query: 486 MMKKGHVSAE 495
            +  G +S +
Sbjct: 478 ALSDGRLSPQ 487



 Score = 75.9 bits (185), Expect = 3e-18
 Identities = 59/231 (25%), Positives = 106/231 (45%), Gaps = 22/231 (9%)

Query: 290 VSFKLHGGEILGVTGLLDSGRNELARALAGVAPAQSGDVLLDGQQIALRTPSDAKRHRIG 349
           +   +  GEI  + G   +G++ L + + GV    +G++   G+++ +R P+ A+   IG
Sbjct: 27  IDLSIQPGEIHALLGENGAGKSTLMKIIYGVTQPDAGEIHWQGERVTMRDPAQARERGIG 86

Query: 350 YVPEDRLNEGLFLDKPIRDNVITAMISS------LRDRFGQIDRTRAQALAEQTVKELQI 403
            V +   +  LF    + +N+  A+ +       L  +  ++ +     L  Q +     
Sbjct: 87  MVFQ---HFSLFETLSVAENIALALGAKAGTPKQLEPKIREVSQRYGMPLEPQRL----- 138

Query: 404 ATPGVDKPVQSLSGGNQQRVLIGRWLAIDPRVLILHGPTVGVDVGSKDIIYRIMQRLSQR 463
                   V SLS G +QRV I R L  D R+LIL  PT  +     D ++  ++RL+  
Sbjct: 139 --------VHSLSIGERQRVEIIRCLMQDIRLLILDEPTSVLTPQEADELFVTLRRLAAE 190

Query: 464 GIGIILISDDLPELLQNCDRILMMKKGHVSAEYRADELSEADLYHALLSEA 514
           G  I+ IS  L E+   C    +++ G VS E    E S+ +L   ++ +A
Sbjct: 191 GCSILFISHKLNEVRALCQSATVLRAGRVSGECIPAECSDLELARLMVGDA 241



 Score = 55.1 bits (131), Expect = 6e-12
 Identities = 58/243 (23%), Positives = 94/243 (38%), Gaps = 25/243 (10%)

Query: 30  ALRGVSLSFQRGQIYHLLGENGCGKSTLIKIISGAQPPDEGQLVI-----EGVPHARLSA 84
           +L+ V L  + G+I  + G  G G+  L+ ++SG Q     Q +      + V H R  A
Sbjct: 274 SLKEVDLEVRAGEIVGIAGVAGNGQDELLALLSGEQRLQAAQAMRIRFLGDDVAHLRPGA 333

Query: 85  LEALA-AGIETVYQDLSLLPNMSVAENVALTSELAT--------HEGRLARTFDRRVLAA 135
                 A +         +P+MS+A+N  LT+   T          GR+ R F  +V+  
Sbjct: 334 RRRHGMAFVPAERLGHGAVPSMSLADNGLLTAYQQTGMVEQGLIRRGRV-RAFAEQVIQR 392

Query: 136 TAARALEAVGLPGNSEFQSTLIEQLPLATRQLVAIARAIASEAKFVIMDEPTTSLTQKEV 195
            A +  +A           T    L     Q   + R I  + K +I   PT  +     
Sbjct: 393 FAVKTPDA----------QTPAASLSGGNLQKFILGREILQQPKLLIAAHPTWGVDVGAA 442

Query: 196 DNLIAVLANLRAQGVTVLFVSHKLDECYAIGGEVIVLRDGQKMAQGPIAEFTKAQISELM 255
             +   L  LR  G  +L +S  L+E + I   +  L DG+   Q   A     ++   M
Sbjct: 443 AAIHRALIELRDAGAAILVISEDLEELFQISDRIAALSDGRLSPQRATASTCPVEVGRWM 502

Query: 256 TGR 258
            G+
Sbjct: 503 AGQ 505


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: 581
Number of extensions: 32
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: 518
Length adjustment: 35
Effective length of query: 480
Effective length of database: 483
Effective search space:   231840
Effective search space used:   231840
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:

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