GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylK_Tm in Pseudomonas fluorescens FW300-N2E3

Align Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale)
to candidate AO353_21385 AO353_21385 D-ribose transporter ATP-binding protein

Query= uniprot:Q9WXX0
         (520 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_21385
          Length = 521

 Score =  419 bits (1078), Expect = e-121
 Identities = 224/504 (44%), Positives = 332/504 (65%), Gaps = 12/504 (2%)

Query: 10  DRMEILKAKGIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAG 69
           D   +L+   + K FPGVVA+ +V   V    +++L+GENGAGKSTL+KI+ G+ +PDAG
Sbjct: 23  DEPYLLEIINVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAG 82

Query: 70  EILVNGERVEFHSPVDAFKKGISVIHQELNLCDNMTVAENIFLAYEAVRGQKRTLSSRVD 129
           E+ + G+ V F +P+ A + GI++IHQELNL  +M++AENI++  E + G        +D
Sbjct: 83  ELRLRGKPVTFDTPLAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNG-----FHMID 137

Query: 130 ENYMYTRSKELLDLIGAKFSPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTV 189
              M+  + +LL+ +     P+  V NL+ A+RQMVEI KA+  +  I+ MDEPTS++T 
Sbjct: 138 HREMHRCTAQLLERLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITD 197

Query: 190 EETERLFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTII 249
           +E   LF II  LK++G  +++++H+++EV  I+D + V RDG  IG  +    D D++I
Sbjct: 198 KEVAHLFSIIADLKAQGKGIIYITHKMNEVFSIADEVAVFRDGAYIGLQRADSMDGDSLI 257

Query: 250 KMMVGREV-EFFPHGIETRP-GEIALEVRNLKWKDKVKNVSFEVRKGEVLGFAGLVGAGR 307
            MMVGRE+ + FP  +  +P G++ + VR+L+     K VSF++  GE+LG AGL+G+GR
Sbjct: 258 SMMVGRELSQLFP--VREKPIGDLLMSVRDLRLDGVFKGVSFDLHAGEILGIAGLMGSGR 315

Query: 308 TETMLLVFGVNQKESGDIYVNGRKVEIKNPEDAIKMGIGLIPEDRKLQGLVLRMTVKDNI 367
           T     +FG+   + G+I ++G+ V I +P  AI+ G  L+ EDRKL GL   ++V +N+
Sbjct: 316 TNVAEAIFGITPSDGGEICLDGQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENM 375

Query: 368 VLPSLKKISRWGLVLDERKEEEISEDYVKRLSIKTPSIYQITENLSGGNQQKVVLAKWLA 427
            +  L   +  G +  ++    + ED  K+L +KTPS+ Q  + LSGGNQQK +LA+WL 
Sbjct: 376 EMAVLPHYAGNGFI-QQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLM 434

Query: 428 TNADILIFDEPTRGIDVGAKAEIHRMIRELAAQGKAVIMISSELPEILNLSDRIVVMWEG 487
           TN  ILI DEPTRGIDVGAKAEI+R+I  LA++G AVIMISSELPE+L +SDR++VM EG
Sbjct: 435 TNPRILILDEPTRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEG 494

Query: 488 EITAVLDNREKRVTQEEIMYYASG 511
           ++   LD  E   TQE +M  ASG
Sbjct: 495 DLMGTLDRSE--ATQERVMQLASG 516



 Score = 96.7 bits (239), Expect = 2e-24
 Identities = 61/233 (26%), Positives = 121/233 (51%), Gaps = 16/233 (6%)

Query: 33  VDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEILVNGERVEFHSPVDAFKKGIS 92
           V F+++  EI+ + G  G+G++ + + + G+   D GEI ++G+ V    P  A +KG +
Sbjct: 295 VSFDLHAGEILGIAGLMGSGRTNVAEAIFGITPSDGGEICLDGQPVRISDPHMAIEKGFA 354

Query: 93  VIHQELNLCDN---MTVAENIFLA---YEAVRG--QKRTLSSRVDENYMYTRSKELLDLI 144
           ++ ++  L      ++V EN+ +A   + A  G  Q++ L +  ++     R K      
Sbjct: 355 LLTEDRKLSGLFPCLSVLENMEMAVLPHYAGNGFIQQKALRALCEDMCKKLRVKTP---- 410

Query: 145 GAKFSPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEETERLFEIIEMLKS 204
               S +  +  L+   +Q   + + L+  PRI+ +DEPT  + V     ++ +I  L S
Sbjct: 411 ----SLEQCIDTLSGGNQQKALLARWLMTNPRILILDEPTRGIDVGAKAEIYRLISYLAS 466

Query: 205 RGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTIIKMMVGREV 257
            G++V+ +S  L EV+ +SDR++VM +G  +G L + E   + ++++  G  V
Sbjct: 467 EGMAVIMISSELPEVLGMSDRVMVMHEGDLMGTLDRSEATQERVMQLASGMSV 519


Lambda     K      H
   0.319    0.138    0.381 

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: 629
Number of extensions: 30
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 520
Length of database: 521
Length adjustment: 35
Effective length of query: 485
Effective length of database: 486
Effective search space:   235710
Effective search space used:   235710
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:

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:

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:

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:

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