GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylK_Tm in Pseudomonas fluorescens FW300-N2C3

Align Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale)
to candidate AO356_23205 AO356_23205 D-ribose transporter ATP-binding protein

Query= uniprot:Q9WXX0
         (520 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_23205
          Length = 517

 Score =  421 bits (1083), Expect = e-122
 Identities = 230/504 (45%), Positives = 328/504 (65%), Gaps = 12/504 (2%)

Query: 10  DRMEILKAKGIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAG 69
           D   +L+   + K FPGVVA+ +V   V    +++L+GENGAGKSTL+KI+ G+ +PDAG
Sbjct: 22  DEPYLLEVVNVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAG 81

Query: 70  EILVNGERVEFHSPVDAFKKGISVIHQELNLCDNMTVAENIFLAYEAVRGQKRTLSSRVD 129
           E+ + G+ V F +P+ A + GI++IHQELNL  +M++AENI++  E + G        VD
Sbjct: 82  ELRLRGKPVTFDTPLAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNGLHM-----VD 136

Query: 130 ENYMYTRSKELLDLIGAKFSPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTV 189
              M+  +  LL+ +  K  P+  V NL+ A+RQMVEI KA+  +  I+ MDEPTS++T 
Sbjct: 137 HGEMHRCTARLLERLRIKLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITE 196

Query: 190 EETERLFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTII 249
            E   LF II  LKS+G  +++++H+++EV  I+D + V RDG  IG  +    D D++I
Sbjct: 197 TEVAHLFSIIADLKSQGKGIIYITHKMNEVFAIADEVAVFRDGAYIGLQRADSMDGDSLI 256

Query: 250 KMMVGREV-EFFPHGIETRP-GEIALEVRNLKWKDKVKNVSFEVRKGEVLGFAGLVGAGR 307
            MMVGRE+ + FP  +  +P GE+ L VR+L      K VSF++  GE+LG AGL+G+GR
Sbjct: 257 SMMVGRELSQLFP--VREQPIGELVLSVRDLSLDGIFKGVSFDLHAGEILGIAGLMGSGR 314

Query: 308 TETMLLVFGVNQKESGDIYVNGRKVEIKNPEDAIKMGIGLIPEDRKLQGLVLRMTVKDNI 367
           T     +FGV     G+I ++G+ V I +P  AI+ G  L+ EDRKL GL   ++V +N+
Sbjct: 315 TNVAEAIFGVTPSTGGEIRLDGQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENM 374

Query: 368 VLPSLKKISRWGLVLDERKEEEISEDYVKRLSIKTPSIYQITENLSGGNQQKVVLAKWLA 427
            +  L      G +  ++    + ED  K+L +KTPS+ Q  + LSGGNQQK +LA+WL 
Sbjct: 375 EMAVLPHYVGNGFI-QQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLM 433

Query: 428 TNADILIFDEPTRGIDVGAKAEIHRMIRELAAQGKAVIMISSELPEILNLSDRIVVMWEG 487
           TN  ILI DEPTRGIDVGAKAEI+R+I  LA++G AVIMISSELPE+L +SDR++VM EG
Sbjct: 434 TNPRILILDEPTRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEG 493

Query: 488 EITAVLDNREKRVTQEEIMYYASG 511
           ++   LD  E   TQE +M  ASG
Sbjct: 494 DLMGTLDRSE--ATQERVMQLASG 515


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: 615
Number of extensions: 26
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 520
Length of database: 517
Length adjustment: 35
Effective length of query: 485
Effective length of database: 482
Effective search space:   233770
Effective search space used:   233770
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