GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hcl in Azospirillum brasilense Sp245

Align 4-hydroxybenzoate--CoA/benzoate--CoA ligase; 4-hydroxybenzoyl-CoA synthetase; EC 6.2.1.25; EC 6.2.1.27 (characterized)
to candidate AZOBR_RS19340 AZOBR_RS19340 long-chain fatty acid--CoA ligase

Query= SwissProt::Q53005
         (539 letters)



>FitnessBrowser__azobra:AZOBR_RS19340
          Length = 519

 Score =  186 bits (471), Expect = 2e-51
 Identities = 159/507 (31%), Positives = 243/507 (47%), Gaps = 31/507 (6%)

Query: 26  AFIDPQRSLSYGELRDAVARVGPMLARLGVEQENRIALVLKDTVDFPILFWGAIRAGIVP 85
           A I  + ++++ EL      V   L   GV + +R+A++L++++++    +GA++AG V 
Sbjct: 21  ALIAGENAVTFAELDRQSDAVACALQSAGVVRGDRVAVMLENSIEYVAGLFGALKAGAVY 80

Query: 86  VLLNTRLTADQYRYLLEDSRSRVVFASSEFLPVIEEAAADLPHLRTIIAVG---DAPAPT 142
           V +N    AD+  Y+L D+  R + A S     +  AA +  HL T + VG    A A  
Sbjct: 81  VPVNPSTKADKLAYILTDAGVRALIAPSALARQVVPAAGEASHLATTLWVGPAVPAGAGG 140

Query: 143 LQLANLLATE---QEGGAPAAT---CADDIAYWQYSSGTTGMPKGVMHVHSSPRVMAENA 196
           L   +++AT    Q GG    +      D+A   Y+SGTTG PKGVM  H++      + 
Sbjct: 141 LSFTDIVATHPDPQSGGTKPQSRGLIDQDLAAILYTSGTTGRPKGVMLSHAALVNTTWSI 200

Query: 197 GRRIGYREDDVVFSAAKLFFAYGLGNAMFCPMGIGATSVLYPERPTADSVFDTLRL--HQ 254
              +    DDVV     L F YGL + +     +G T VL  ER  A       R+  H+
Sbjct: 201 STYLENTPDDVVMCVLPLTFGYGL-SQILTGARVGFTVVL--ERSFAFPAETLARMVKHR 257

Query: 255 PTLLFAVPTLYAAMLADPRSRTETLPDRLRLCVSAGEPLPAQVGLNWRNRFGHDIVNGV- 313
            T L  VPT ++ +L     +T  L   LR   +A  PLP       R RF       + 
Sbjct: 258 ITGLPGVPTFFSTLLGMEALKTADL-SSLRYLTNAAAPLPTAHIDRLRERFPDAAFYSMY 316

Query: 314 GSTE--MGHLFLTNLPHAVEYGTSGVPVDGYRLRLVGDRGQDVADDEIGELLVSGGSSAA 371
           G TE      +L       +  + G  +      +V + G   A  E+GEL+V G +   
Sbjct: 317 GMTECCTRICYLDPRDLGTKTASVGRAIPNCEAYVVDELGNRAAPGEVGELVVRGANVMR 376

Query: 372 GYWNQRDKT----RTTFVGE-WTRTGDKYHRRADGVYTYCGRTDDIFKVSGIWVSPFEIE 426
           GYWN+ ++T    R+   GE    TGD +   ADG   +  R DD+FK  G  VSP E+E
Sbjct: 377 GYWNRPEETAKRLRSGPQGETLLYTGDLFTMDADGCLYFVSRKDDVFKCRGEKVSPKEVE 436

Query: 427 QALMSHAKVLEAAVIPAEDTDGLIKPKAFIVLASRGDIDPGALFDE--LKEHVKSAIGPW 484
            AL     V+EAAV+   D+   +  KA++V      + PGA   E  +++H +  +   
Sbjct: 437 NALYELEAVVEAAVLGVPDSADGMAVKAYLV------VRPGATLTEMAIRQHCRGRLESH 490

Query: 485 KYPRWIQIMDDLPKTSSGKLQRYLLRE 511
             P++I+I D+LPKT SGK++R +L E
Sbjct: 491 LVPKFIEIRDELPKTESGKIKRAMLAE 517


Lambda     K      H
   0.320    0.138    0.415 

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: 670
Number of extensions: 35
Number of successful extensions: 6
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: 539
Length of database: 519
Length adjustment: 35
Effective length of query: 504
Effective length of database: 484
Effective search space:   243936
Effective search space used:   243936
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 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