Alignments for a candidate for H281DRAFT_01113 in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Alignments for a candidate for H281DRAFT_01113 in Pseudomonas simiae WCS417

Align deoxynucleoside transporter, ATPase component (characterized)
to candidate GFF2332 PS417_11890 D-ribose transporter ATP-binding protein

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



>FitnessBrowser__WCS417:GFF2332
          Length = 517

 Score =  327 bits (838), Expect = 6e-94
 Identities = 186/508 (36%), Positives = 291/508 (57%), Gaps = 15/508 (2%)

Query: 3   QQEVSSAPLSQP-------FLEVVGVHKRFTGVHALRGVSLSFQRGQIYHLLGENGCGKS 55
           Q  VS  P  QP        LE+V + K F GV AL  V L  + G +  L+GENG GKS
Sbjct: 4   QATVSQPPSLQPQTLEEPYLLEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKS 63

Query: 56  TLIKIISGAQPPDEGQLVIEGVPHARLSALEALAAGIETVYQDLSLLPNMSVAENVALTS 115
           TL+KII+G   PD G++ + G P    + L A  AGI  ++Q+L+L+P+MS+AEN+ +  
Sbjct: 64  TLMKIIAGIYQPDAGEIRLRGKPIVFETPLAAQKAGIAMIHQELNLMPHMSIAENIWIGR 123

Query: 116 ELATHEGRLARTFDRRVLAATAARALEAVGLPGNSEFQSTLIEQLPLATRQLVAIARAIA 175
           E            + R +    A  L  + +  + E Q   +  L +A RQ+V IA+A++
Sbjct: 124 EQLNS----LHMVNHREMHRCTAELLARLRINLDPEEQ---VGNLSIAERQMVEIAKAVS 176

Query: 176 SEAKFVIMDEPTTSLTQKEVDNLIAVLANLRAQGVTVLFVSHKLDECYAIGGEVIVLRDG 235
            ++  +IMDEPT+++T+KEV +L +++A+L++QG  +++++HK++E +AI  EV V RDG
Sbjct: 177 YDSDILIMDEPTSAITEKEVAHLFSIIADLKSQGKGIVYITHKMNEVFAIADEVAVFRDG 236

Query: 236 QKMAQGPIAEFTKAQISELMTGRHLSNERYRESAHAQDIVLDVRGFTRAGQFSDVSFKLH 295
             +            +  +M GR LS           D++L VR  T  G F DVSF LH
Sbjct: 237 HYIGLQRADSMNSDSLISMMVGRELSQLFPLRETPIGDLLLTVRDLTLDGVFKDVSFDLH 296

Query: 296 GGEILGVTGLLDSGRNELARALAGVAPAQSGDVLLDGQQIALRTPSDAKRHRIGYVPEDR 355
            GEILG+ GL+ SGR  +A  + G+ P+ SG + LDG+ + +  P  A       + EDR
Sbjct: 297 AGEILGIAGLMGSGRTNVAETIFGITPSSSGQITLDGKAVRISDPHMAIEKGFALLTEDR 356

Query: 356 LNEGLFLDKPIRDNVITAMISSLRDRFGQIDRTRAQALAEQTVKELQIATPGVDKPVQSL 415
              GLF    + +N+  A++       G I +   +AL E   K+L++ TP +++ + +L
Sbjct: 357 KLSGLFPCLSVLENMEMAVLPHYTGN-GFIQQKALRALCEDMCKKLRVKTPSLEQCIDTL 415

Query: 416 SGGNQQRVLIGRWLAIDPRVLILHGPTVGVDVGSKDIIYRIMQRLSQRGIGIILISDDLP 475
           SGGNQQ+ L+ RWL  +PR+LIL  PT G+DVG+K  IYR++  L+  G+ +I+IS +LP
Sbjct: 416 SGGNQQKALLARWLMTNPRLLILDEPTRGIDVGAKAEIYRLIAFLASEGMAVIMISSELP 475

Query: 476 ELLQNCDRILMMKKGHVSAEYRADELSE 503
           E+L   DR+++M +G +       E ++
Sbjct: 476 EVLGMSDRVMVMHEGELMGTLDRSEATQ 503



 Score = 70.5 bits (171), Expect = 1e-16
 Identities = 56/242 (23%), Positives = 110/242 (45%), Gaps = 10/242 (4%)

Query: 267 ESAHAQDIVLDVRGFTRAGQFSDVSFKLHGGEILGVTGLLDSGRNELARALAGVAPAQSG 326
           E  +  +IV   +GF      +DV  ++  G +L + G   +G++ L + +AG+    +G
Sbjct: 19  EEPYLLEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDAG 78

Query: 327 DVLLDGQQIALRTPSDAKRHRIGYVPEDRLNEGLFLDKPIRDNVITAMISSLRDRFGQID 386
           ++ L G+ I   TP  A++  I  + ++ LN  L     I +N+        R++   + 
Sbjct: 79  EIRLRGKPIVFETPLAAQKAGIAMIHQE-LN--LMPHMSIAENIWIG-----REQLNSLH 130

Query: 387 RTRAQALAEQTVKELQIATPGVD--KPVQSLSGGNQQRVLIGRWLAIDPRVLILHGPTVG 444
               + +   T + L      +D  + V +LS   +Q V I + ++ D  +LI+  PT  
Sbjct: 131 MVNHREMHRCTAELLARLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSA 190

Query: 445 VDVGSKDIIYRIMQRLSQRGIGIILISDDLPELLQNCDRILMMKKGHVSAEYRADELSEA 504
           +       ++ I+  L  +G GI+ I+  + E+    D + + + GH     RAD ++  
Sbjct: 191 ITEKEVAHLFSIIADLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNSD 250

Query: 505 DL 506
            L
Sbjct: 251 SL 252



 Score = 65.9 bits (159), Expect = 3e-15
 Identities = 53/229 (23%), Positives = 105/229 (45%), Gaps = 8/229 (3%)

Query: 32  RGVSLSFQRGQIYHLLGENGCGKSTLIKIISGAQPPDEGQLVIEGVPHARLSALEALAAG 91
           + VS     G+I  + G  G G++ + + I G  P   GQ+ ++G          A+  G
Sbjct: 289 KDVSFDLHAGEILGIAGLMGSGRTNVAETIFGITPSSSGQITLDGKAVRISDPHMAIEKG 348

Query: 92  IETVYQDLSL---LPNMSVAENVALTSELATHEGRLARTFDRRVLAATAARALEAVGLPG 148
              + +D  L    P +SV EN+ + + L  + G       ++ L A      + + +  
Sbjct: 349 FALLTEDRKLSGLFPCLSVLENMEM-AVLPHYTGN--GFIQQKALRALCEDMCKKLRVKT 405

Query: 149 NSEFQSTLIEQLPLATRQLVAIARAIASEAKFVIMDEPTTSLTQKEVDNLIAVLANLRAQ 208
            S  Q   I+ L    +Q   +AR + +  + +I+DEPT  +       +  ++A L ++
Sbjct: 406 PSLEQC--IDTLSGGNQQKALLARWLMTNPRLLILDEPTRGIDVGAKAEIYRLIAFLASE 463

Query: 209 GVTVLFVSHKLDECYAIGGEVIVLRDGQKMAQGPIAEFTKAQISELMTG 257
           G+ V+ +S +L E   +   V+V+ +G+ M     +E T+ ++ +L +G
Sbjct: 464 GMAVIMISSELPEVLGMSDRVMVMHEGELMGTLDRSEATQEKVMQLASG 512


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: 562
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: 515
Length of database: 517
Length adjustment: 35
Effective length of query: 480
Effective length of database: 482
Effective search space:   231360
Effective search space used:   231360
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