GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rbsA in Thiothrix lacustris DSM 21227

Align ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 (characterized)
to candidate WP_028489030.1 Q394_RS0109195 ABC transporter ATP-binding protein

Query= CharProtDB::CH_003578
         (501 letters)



>NCBI__GCF_000621325.1:WP_028489030.1
          Length = 348

 Score = 92.4 bits (228), Expect = 2e-23
 Identities = 64/222 (28%), Positives = 102/222 (45%), Gaps = 20/222 (9%)

Query: 3   ALLQLKGIDKAFPGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDAGTLL 62
           A L+LK +DK +  + A+   +L +  G  +  VG +G GKST+++++ G+   + G L+
Sbjct: 2   AFLELKNVDKYYGKLHAIKQVSLEIQSGEFIVFVGPSGCGKSTLLRMIAGLEVINGGQLI 61

Query: 63  WLGKETTFTGPKSSQEAGIGIIHQELNLIPQLTIAENIFLGREFVNRFGKIDWKTMYAEA 122
             G++ T   P    +  + ++ Q   L P +T+ EN+     F  R  K+D   +  + 
Sbjct: 62  LDGRDITEVPP---SQRDLAMVFQSYALYPHMTVEENM----SFALRLAKVDPAIIQEKV 114

Query: 123 DKLLAKLNLRFKSDKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDAL-------TDT 175
                KLNL     +    LS G +Q V I + +    KV + DEP   L       T  
Sbjct: 115 KMAADKLNLTAYLQRTPKALSGGQRQRVAIGRSIVRSPKVFLFDEPLSNLDAALRGNTRV 174

Query: 176 ETESLFRVIRELKSQGRGIVYISHRMKEIFEICDDVTVFRDG 217
           E  SL R +      G   VY++H   E   + D V V RDG
Sbjct: 175 EIASLHREL------GATTVYVTHDQVEAMTLADRVVVLRDG 210



 Score = 70.9 bits (172), Expect = 7e-17
 Identities = 53/205 (25%), Positives = 98/205 (47%), Gaps = 14/205 (6%)

Query: 268 VNDVSFTLRKGEILGVSGLMGAGRTELMKVLYGALPRTSGYVTLDGHEVVTRSPQDGLAN 327
           +  VS  ++ GE +   G  G G++ L++++ G      G + LDG ++ T  P      
Sbjct: 19  IKQVSLEIQSGEFIVFVGPSGCGKSTLLRMIAGLEVINGGQLILDGRDI-TEVPPSQRDL 77

Query: 328 GIVYISEDRKRDGLVLGMSVKENMSLTALRYFSRAGGSLKHADEQQAVSDFIRLFNVKTP 387
            +V+ S       L   M+V+ENMS  ALR        ++   +  A    +  +  +TP
Sbjct: 78  AMVFQSY-----ALYPHMTVEENMSF-ALRLAKVDPAIIQEKVKMAADKLNLTAYLQRTP 131

Query: 388 SMEQAIGLLSGGNQQKVAIARGLMTRPKVLILDEPTRGVDVGAKKEI-YQLINQFKADGL 446
                   LSGG +Q+VAI R ++  PKV + DEP   +D   +     ++ +  +  G 
Sbjct: 132 KA------LSGGQRQRVAIGRSIVRSPKVFLFDEPLSNLDAALRGNTRVEIASLHRELGA 185

Query: 447 SIILVSSEMPEVLGMSDRIIVMHEG 471
           + + V+ +  E + ++DR++V+ +G
Sbjct: 186 TTVYVTHDQVEAMTLADRVVVLRDG 210


Lambda     K      H
   0.318    0.137    0.380 

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: 373
Number of extensions: 18
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 2
Length of query: 501
Length of database: 348
Length adjustment: 31
Effective length of query: 470
Effective length of database: 317
Effective search space:   148990
Effective search space used:   148990
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Apr 09 2024. 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