GapMind for catabolism of small carbon sources

 

Alignments for a candidate for BPHYT_RS16930 in Bradyrhizobium sp. BTAi1

Align Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale)
to candidate WP_012042345.1 BBTA_RS09915 sugar ABC transporter ATP-binding protein

Query= uniprot:B2SYR5
         (512 letters)



>NCBI__GCF_000015165.1:WP_012042345.1
          Length = 516

 Score =  353 bits (907), Expect = e-102
 Identities = 200/496 (40%), Positives = 306/496 (61%), Gaps = 12/496 (2%)

Query: 5   LRFDNIGKVFPGVRALDGVSFDVNVGQVHGLMGENGAGKSTLLKILGGEYQPDSGRVMID 64
           L    + K F  ++AL  V F +  G++H L+GENGAGKSTL+K++ G +  D+G V + 
Sbjct: 15  LEIRGLTKSFGALKALQDVDFTLGEGEIHALLGENGAGKSTLIKVVTGVFARDAGTVRLA 74

Query: 65  GNEVRFTSAASSIAAGIAVIHQELQYVPDLTVAENLLLGQLPNSLGWVNKREAKRFVRER 124
           G+E+   SA  ++ AGIA ++QE+  +P+L+VA+NL LG+ P   G V + E +R     
Sbjct: 75  GDEIAPRSAKDAVEAGIATVYQEVNLLPNLSVAQNLYLGRQPTRFGVVRQAEMRRRAHAL 134

Query: 125 LEAMGVALDPNAKLRKLSIAQRQMVEICKALLRNARVIALDEPTSSLSHRETEVLFKLVR 184
           L   G+ +D  A L   S+A + +  I +A+  +ARV+ LDEPT+SL   E E+LF+++R
Sbjct: 135 LLDYGLDIDVGAPLASYSVAVQHITAIARAVDLSARVLILDEPTASLDRHEVEILFRVMR 194

Query: 185 DLRADNRAMIYISHRMDEIYELCDACTIFRDGRKIASHPTLEGVTRDTIVSEMVGREISD 244
            L AD   ++++SH +D++YE+CD  T+ R+GR I +   +  + R  ++  M+GRE+++
Sbjct: 195 KLAADGIGIVFVSHFLDQVYEICDRVTVLRNGRLIGTR-DITDLPRLDLIRMMLGRELAE 253

Query: 245 IYNYSAR----PLGEVRFAAKGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSELMHLVY 300
             +  A        EV  + KG        P   E+RRGE+VG  GL+G+GR+E   LV+
Sbjct: 254 TTHERAASQPDTAREVCVSFKGFGKQGYVAPFDLELRRGEVVGLAGLLGSGRTETARLVF 313

Query: 301 GADHKKGGELLLDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISCRRHY 360
           GA+    GE  + GK +++ S  +A   G   CPE+RK EGIVA  TV ENI ++ +   
Sbjct: 314 GAERADSGEASVAGKAVRLNSPRDAAGLGFGYCPEERKTEGIVADLTVRENIVLALQ--- 370

Query: 361 LRVGMF--LDRKKEAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSRWLAEPDLKV 418
            R G+   L R+++ E A R+I++L I+ P   + I  LSGGNQQKA+L+RWLA    K+
Sbjct: 371 ARRGLHRPLSRREQDEIAMRYIRMLDIRPPDPERPIGLLSGGNQQKALLARWLATSP-KL 429

Query: 419 VILDEPTRGIDVGAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRISGE 478
           ++LDEPTRGIDVGA  EI  ++  L E+G A+++ISSEL E++  S+R+VV+R  R   E
Sbjct: 430 LVLDEPTRGIDVGAHAEIIRLVRDLCEQGLALLVISSELDEIVTYSNRVVVLRD-RAHVE 488

Query: 479 LTRKDATEQSVLSLAL 494
             + DA E S +  A+
Sbjct: 489 ELKGDAVEVSSILAAI 504



 Score = 75.5 bits (184), Expect = 4e-18
 Identities = 73/269 (27%), Positives = 118/269 (43%), Gaps = 23/269 (8%)

Query: 249 SARP-LGEVRFAAKGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSELMHLVYGADHKKG 307
           +ARP L E+R   K        Q   F +  GEI    G  GAG+S L+ +V G   +  
Sbjct: 9   AARPSLLEIRGLTKSFGALKALQDVDFTLGEGEIHALLGENGAGKSTLIKVVTGVFARDA 68

Query: 308 GELLLDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISCRRHYLRVGMFL 367
           G + L G  I  RSA +A+  GI    +   E  ++   +V++N+ +   R   R G+  
Sbjct: 69  GTVRLAGDEIAPRSAKDAVEAGIATVYQ---EVNLLPNLSVAQNLYLG--RQPTRFGVV- 122

Query: 368 DRKKEAETADRFIKLL-------KIKTPSRRQKIRFLSGGNQQKAILSRWLAEPDLKVVI 420
              ++AE   R   LL        +  P     +       Q    ++R   +   +V+I
Sbjct: 123 ---RQAEMRRRAHALLLDYGLDIDVGAPLASYSVAV-----QHITAIAR-AVDLSARVLI 173

Query: 421 LDEPTRGIDVGAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRISGELT 480
           LDEPT  +D      ++ V+ +LA  G  IV +S  L +V  + DR+ V+R GR+ G   
Sbjct: 174 LDEPTASLDRHEVEILFRVMRKLAADGIGIVFVSHFLDQVYEICDRVTVLRNGRLIGTRD 233

Query: 481 RKDATEQSVLSLALPQSSTALPGTQAAAQ 509
             D     ++ + L +        +AA+Q
Sbjct: 234 ITDLPRLDLIRMMLGRELAETTHERAASQ 262


Lambda     K      H
   0.320    0.136    0.385 

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: 644
Number of extensions: 37
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: 2
Length of query: 512
Length of database: 516
Length adjustment: 35
Effective length of query: 477
Effective length of database: 481
Effective search space:   229437
Effective search space used:   229437
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 (21.8 bits)
S2: 52 (24.6 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