Alignments for a candidate for ytfR in Azospirillum brasilense Sp245

GapMind for catabolism of small carbon sources

Alignments for a candidate for ytfR in Azospirillum brasilense Sp245

Align galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized)
to candidate AZOBR_RS06950 AZOBR_RS06950 ABC transporter

Query= ecocyc::YTFR-MONOMER
         (500 letters)



>FitnessBrowser__azobra:AZOBR_RS06950
          Length = 520

 Score =  266 bits (681), Expect = 1e-75
 Identities = 168/472 (35%), Positives = 253/472 (53%), Gaps = 10/472 (2%)

Query: 10  LRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWLE 69
           L   G++K FPG  A D VD  LR GEI ALLGENGAGKSTL+K + GV HAD G I   
Sbjct: 13  LELRGITKRFPGCLANDQVDLVLRPGEIHALLGENGAGKSTLVKIIYGVLHADAGRIQWN 72

Query: 70  GQAISPKNTAHAQQLGIGTVYQEVNLLPNMSVADNLFIGREPKRFGLLRRKEMEKRATEL 129
           G      + A A++LGIG V+Q  +L   ++VA+N+ +G +    G +    +  R  E+
Sbjct: 73  GHDTHIPDPAGARRLGIGMVFQHFSLFDTLTVAENISLGLDQP--GPI--DALSARIAEV 128

Query: 130 MASYGFSLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLFDLMR 189
              YG SLD R  ++  SV  +Q V I R +    K+LI+DEPT+ L  QE   LF+ +R
Sbjct: 129 SERYGLSLDPRRHVHNLSVGERQRVEIVRCLLQDPKLLIMDEPTSVLTPQEATRLFETLR 188

Query: 190 QLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMMLGRELDTH 249
           +L   G ++++++H L+++  + D  TVLR G  VG  +        L +MM+G EL T 
Sbjct: 189 RLAAEGCTILYISHKLEEIRALCDTATVLRGGRVVGSCDPRRETARSLAEMMIGTELSTP 248

Query: 250 ---ALQRAGRTLLSDKPVAAFKNYGKKGTIAPFDLEVRPGEIVGLAGLLGSGRTETAEVI 306
                  AG   L  + ++   +      +     EVR GEI+G+AG+ G+G+ E    +
Sbjct: 249 ERLPQGEAGAAKLQVRHLSTTSDNPFATNLKDVSFEVRAGEILGIAGVAGNGQAELMAAL 308

Query: 307 FG-IKPADSGTALIKGKPQNLRSPHQASVLGIGFCPEDRKTDGIIAAASVRENIILALQA 365
            G     D  +  I+G+P     P +  +LG+ F PE+R   G +   S+ EN +L+  A
Sbjct: 309 SGEALVPDPASVAIEGRPAGHLGPRERRLLGLAFVPEERLGRGAVPELSLSENALLSGYA 368

Query: 366 QRGWLRP--ISRKEQQEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKVLLSRWLLTRPQF 423
           +   +R   +     +  AER I    + T         LSGGN QK ++ R +L +P+ 
Sbjct: 369 REPLVRSGLVHFGRARSYAERIIGAFNVVTHGHRAEARSLSGGNLQKFIIGREILQKPRL 428

Query: 424 LILDEPTRGIDVGAHAEIIRLIETLCADGLALLVISSELEELVGYADRVIIM 475
           L++ +PT G+D GA A I R +  L   G A+LVIS +L+EL   +DR+ ++
Sbjct: 429 LVVGQPTWGVDAGAAAAIHRALIDLARAGAAVLVISQDLDELFVLSDRIAVL 480



 Score = 85.1 bits (209), Expect = 5e-21
 Identities = 64/202 (31%), Positives = 101/202 (50%), Gaps = 10/202 (4%)

Query: 280 DLEVRPGEIVGLAGLLGSGRTETAEVIFGIKPADSGTALIKGKPQNLRSPHQASVLGIGF 339
           DL +RPGEI  L G  G+G++   ++I+G+  AD+G     G   ++  P  A  LGIG 
Sbjct: 32  DLVLRPGEIHALLGENGAGKSTLVKIIYGVLHADAGRIQWNGHDTHIPDPAGARRLGIGM 91

Query: 340 CPEDRKTDGIIAAASVRENIILALQAQRGWLRPISRKEQQEIAERFIRQLGIRTPSTEQP 399
             +      +    +V ENI L L  Q G +  +S +   E++ER+   L  R     + 
Sbjct: 92  VFQHFS---LFDTLTVAENISLGLD-QPGPIDALSARIA-EVSERYGLSLDPR-----RH 141

Query: 400 IEFLSGGNQQKVLLSRWLLTRPQFLILDEPTRGIDVGAHAEIIRLIETLCADGLALLVIS 459
           +  LS G +Q+V + R LL  P+ LI+DEPT  +       +   +  L A+G  +L IS
Sbjct: 142 VHNLSVGERQRVEIVRCLLQDPKLLIMDEPTSVLTPQEATRLFETLRRLAAEGCTILYIS 201

Query: 460 SELEELVGYADRVIIMRDRKQV 481
            +LEE+    D   ++R  + V
Sbjct: 202 HKLEEIRALCDTATVLRGGRVV 223



 Score = 63.9 bits (154), Expect = 1e-14
 Identities = 57/233 (24%), Positives = 107/233 (45%), Gaps = 10/233 (4%)

Query: 20  PGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTG-VYHADRGTIWLEGQAISPKNT 78
           P    L +V F +R GEI+ + G  G G++ L+ AL+G     D  ++ +EG+       
Sbjct: 273 PFATNLKDVSFEVRAGEILGIAGVAGNGQAELMAALSGEALVPDPASVAIEGRPAGHLGP 332

Query: 79  AHAQQLGIGTVYQEV---NLLPNMSVADNLFIG---REPK-RFGLLRRKEMEKRATELMA 131
              + LG+  V +E      +P +S+++N  +    REP  R GL+        A  ++ 
Sbjct: 333 RERRLLGLAFVPEERLGRGAVPELSLSENALLSGYAREPLVRSGLVHFGRARSYAERIIG 392

Query: 132 SYGF-SLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLFDLMRQ 190
           ++   +   R      S    Q   I R I    ++L++ +PT  +D      +   +  
Sbjct: 393 AFNVVTHGHRAEARSLSGGNLQKFIIGREILQKPRLLVVGQPTWGVDAGAAAAIHRALID 452

Query: 191 LRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMMLG 243
           L   G +++ ++  LD+++ +SDRI VL +G     R T     +E + +++G
Sbjct: 453 LARAGAAVLVISQDLDELFVLSDRIAVLFHGHLSESRPT-HHTSVEEIGLLMG 504


Lambda     K      H
   0.321    0.138    0.391 

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: 574
Number of extensions: 32
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: 3
Length of query: 500
Length of database: 520
Length adjustment: 34
Effective length of query: 466
Effective length of database: 486
Effective search space:   226476
Effective search space used:   226476
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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources