Aligments for a candidate for araG in Azospirillum brasilense Sp245

GapMind for catabolism of small carbon sources

Aligments for a candidate for araG in Azospirillum brasilense Sp245

Align L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized)
to candidate AZOBR_RS31210 AZOBR_RS31210 sugar ABC transporter ATP-binding protein

Query= CharProtDB::CH_014279
         (504 letters)



>FitnessBrowser__azobra:AZOBR_RS31210
          Length = 516

 Score =  345 bits (886), Expect = 2e-99
 Identities = 204/516 (39%), Positives = 307/516 (59%), Gaps = 30/516 (5%)

Query: 4   STPYLSFRGIGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGS 63
           S P L+ RG+ K F GV+AL  + F    G++HAL+GENGAGKSTL+K L+G Y    G+
Sbjct: 9   SPPLLAIRGLSKAFLGVQALDGVDFTVRHGEIHALLGENGAGKSTLIKTLTGVYQRDAGT 68

Query: 64  VVINGQEMSFSDTTAALNAGVAIIYQELHLVPEMTVAENIYLGQLPHKGGIVNRSLLNYE 123
           V + G+ ++      A    +  +YQE++L+P ++VAEN++LG+ P + G+V+R  +   
Sbjct: 69  VTLEGRAIAPRGVEEAQRLHIGTVYQEVNLLPNLSVAENLFLGRQPMRFGLVDRGAMRRR 128

Query: 124 AGLQLKHLGMDIDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDNLF 183
           A   L   G+ +D   PL   S+   Q+V IA+A+  +AK++  DEPT+SL A+E+  LF
Sbjct: 129 ARAVLIPYGLTLDVTAPLGRFSVATQQIVAIARAVDMSAKVLILDEPTASLDAQEVAVLF 188

Query: 184 RVIRELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYV--KTFTDMQQVDHDALVQAMV 241
           +V+R LR  G  I++V+H +++++AL D ITV ++GR V  +   ++ ++D   LV  M+
Sbjct: 189 KVMRTLRSRGIGIVFVTHFLDQVYALCDRITVLRNGRLVGERRTAELPRLD---LVAMML 245

Query: 242 GRDIGDIYG--WQPRSYGEERLRLDAVKAPGVR-----TPISLAVRSGEIVGLFGLVGAG 294
           GR++  +      P    EE  R   V+  G        P  L +R GE+VGL GL+G+G
Sbjct: 246 GRELEAVAHRIAPPADDAEEDARPPLVRFRGYGKARSVEPFDLDIRPGEVVGLAGLLGSG 305

Query: 295 RSELMKGMFGGTQITAGQVYIDQQPIDIRKPSHAIAAGMMLCPEDRKAEGIIPVHSVRDN 354
           R+E  + +FG  +   G+  +D Q + +R P  AI  G   CPEDRK EGI+   SVR+N
Sbjct: 306 RTETARLVFGMDRADRGEAAVDGQAVRLRGPRDAIRLGFGFCPEDRKKEGIVGALSVREN 365

Query: 355 INISARRKHVLGGCVINNGW--------EENNADHHIRSLNIKTPGAEQLIMNLSGGNQQ 406
           I ++ + +          GW        +E  AD  IR L+I+TP AEQ I  LSGGNQQ
Sbjct: 366 IILALQAR---------QGWLRPIPRCRQEEIADRFIRLLDIRTPHAEQPIQLLSGGNQQ 416

Query: 407 KAILGRWLSEEMKVILLDEPTRGIDVGAKHEIYNVIYALAAQGVAVLFASSDLPEVLGVA 466
           KA+L RWL+ E ++++LDEPTRGIDVGA  EI  +I  L A G+A+L  SS+L E++  +
Sbjct: 417 KALLARWLATEPRLLILDEPTRGIDVGAHAEIIRLIERLCADGMALLVVSSELEEIVAYS 476

Query: 467 DRIVVMREGEIAGELL-HEQADERQALSLAMPKVSQ 501
            R+VV+R+     EL   E A +R   ++A   V +
Sbjct: 477 RRVVVLRDRRHVAELRGGEVAVDRIVAAIASESVPE 512



 Score = 70.9 bits (172), Expect = 1e-16
 Identities = 60/233 (25%), Positives = 106/233 (45%), Gaps = 13/233 (5%)

Query: 275 ISLAVRSGEIVGLFGLVGAGRSELMKGMFGGTQITAGQVYIDQQPIDIRKPSHAIAAGMM 334
           +   VR GEI  L G  GAG+S L+K + G  Q  AG V ++ + I  R    A    + 
Sbjct: 31  VDFTVRHGEIHALLGENGAGKSTLIKTLTGVYQRDAGTVTLEGRAIAPRGVEEAQRLHIG 90

Query: 335 LCPEDRKAEGIIPVHSVRDNINISARRKHVLGGCVINNGWEENNADHHIR---SLNIKTP 391
              ++     ++P  SV +N+ +   R+ +  G V             I    +L++  P
Sbjct: 91  TVYQE---VNLLPNLSVAENLFLG--RQPMRFGLVDRGAMRRRARAVLIPYGLTLDVTAP 145

Query: 392 GAEQLIMNLSGGNQQKAILGRWLSEEMKVILLDEPTRGIDVGAKHEIYNVIYALAAQGVA 451
                +   S   QQ   + R +    KV++LDEPT  +D      ++ V+  L ++G+ 
Sbjct: 146 -----LGRFSVATQQIVAIARAVDMSAKVLILDEPTASLDAQEVAVLFKVMRTLRSRGIG 200

Query: 452 VLFASSDLPEVLGVADRIVVMREGEIAGELLHEQADERQALSLAMPKVSQAVA 504
           ++F +  L +V  + DRI V+R G + GE    +      +++ + +  +AVA
Sbjct: 201 IVFVTHFLDQVYALCDRITVLRNGRLVGERRTAELPRLDLVAMMLGRELEAVA 253


Lambda     K      H
   0.319    0.136    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: 635
Number of extensions: 31
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 504
Length of database: 516
Length adjustment: 34
Effective length of query: 470
Effective length of database: 482
Effective search space:   226540
Effective search space used:   226540
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:

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, or view the source code.

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