Alignments for a candidate for BPHYT_RS34245 in Azospirillum brasilense Sp245

GapMind for catabolism of small carbon sources

Alignments for a candidate for BPHYT_RS34245 in Azospirillum brasilense Sp245

Align ABC transporter related; Flags: Precursor (characterized, see rationale)
to candidate AZOBR_RS31245 AZOBR_RS31245 ABC transporter ATP-binding protein

Query= uniprot:B2T9V9
         (510 letters)



>FitnessBrowser__azobra:AZOBR_RS31245
          Length = 518

 Score =  253 bits (645), Expect = 2e-71
 Identities = 163/498 (32%), Positives = 266/498 (53%), Gaps = 24/498 (4%)

Query: 11  SVPVVEALEVTKRFGSTAALNDVSIRVMPGESHALVGRNGAGKSTLVSILTGLRKPDT-- 68
           ++P++E   +TK F    AL+DV++ V  GE HAL+G NGAGKSTL+ +L+G+    +  
Sbjct: 2   AMPILEMKGITKTFPGVKALDDVNLSVREGEIHALIGENGAGKSTLMKVLSGVYPQGSFD 61

Query: 69  GEVRFSGAAAPSIADRDAWRERVACVYQHSTIIRDLSVAENLFINRQPLRGGVIDWQAMR 128
           GE+RF G         D+ R  +  ++Q   ++  LS+ ENLF+  +    GVIDW A  
Sbjct: 62  GEIRFRGQPQAFRGIADSERLGIIIIHQELALVPLLSITENLFLGNEQASRGVIDWDAAT 121

Query: 129 RDARALLDHWKIDVREDARAGDLSVEARQLVEIARALSYGARFIILDEPTAQLDGDEIKR 188
             AR LL    +    +    D+ V  +QLVEIA+ALS   + +ILDEPTA L+  +   
Sbjct: 122 LRARELLRLVGLHDPPETLITDIGVGKQQLVEIAKALSKEVKLLILDEPTASLNESDSDA 181

Query: 189 LFRRISELQREGVTFLFISHHLQEVYEICQAVTVLRDARHI--VSAPVSALPREQLIEAM 246
           L   + + +  G+  + ISH L E+ ++   VT+LRD   +  +    + + ++++I  M
Sbjct: 182 LLELLLQFKARGIASILISHKLNEIAKVADRVTILRDGTTVETLDCREAVVSQDRIIRGM 241

Query: 247 TGERGGLAVADA-AARGALPADTAVALELKELTGADY---------EGVSFTVKRGEVVG 296
            G     A++D    R  +P D  V  E+K  + AD+           V+ TV+RGEVVG
Sbjct: 242 VGR----ALSDRYPRRTTVPGD--VLFEVKGWS-ADHPAHPGRRVVRDVNLTVRRGEVVG 294

Query: 297 LTGATSSGRTSVAEAIAGLRAAK--RGTISVDGAILPPGDVPASLAHGIGCVPKDRHHEG 354
           + G   +GRT  A ++ G    +  RG   +DG  +    +  ++A+G+    +DR H G
Sbjct: 295 IAGLMGAGRTEFAMSLFGRSYGRNIRGQAFLDGREIDVSTISRAMANGLAYATEDRKHLG 354

Query: 355 LVLTQSVAENASMTIARVLGKFGIAAPAKKNAFGQKMIDALGIVAQGPEHVVSGLSGGNQ 414
           LVL   +  N ++   R + K  +    ++    ++    L I           LSGGNQ
Sbjct: 355 LVLDNDIRHNVTLANLRGVAKRWVIDHEREVQVAEEFRRRLRIRCADVFQETVNLSGGNQ 414

Query: 415 QKVVMARALATNPNVLVLIDPTAGVDVKSKEALLSVVDRVREEGKAVLVVSGELDD-LRT 473
           QKVV+++ L  +P VL+L +PT G+DV +K  + ++++++  EG+ V+++S E+ + L  
Sbjct: 415 QKVVLSKWLFADPQVLILDEPTRGIDVGAKYEIYTIINQLVAEGRGVVLISSEMPELLGV 474

Query: 474 CDRVLVMFRGRVAAEFPA 491
            DR+ VM  G + AE PA
Sbjct: 475 ADRIYVMNAGEMVAEMPA 492



 Score = 41.2 bits (95), Expect = 9e-08
 Identities = 50/236 (21%), Positives = 95/236 (40%), Gaps = 30/236 (12%)

Query: 30  LNDVSIRVMPGESHALVGRNGAGKSTLVSILTGLR--KPDTGEVRFSGAAAPSIADRDAW 87
           + DV++ V  GE   + G  GAG++     L G    +   G+    G          A 
Sbjct: 280 VRDVNLTVRRGEVVGIAGLMGAGRTEFAMSLFGRSYGRNIRGQAFLDGREIDVSTISRAM 339

Query: 88  RERVACVYQ---HSTIIRDLSVAENLFINRQPLRGGVIDWQAMRRDARALLDHWK-IDVR 143
              +A   +   H  ++ D  +  N+ +    LRG    W         ++DH + + V 
Sbjct: 340 ANGLAYATEDRKHLGLVLDNDIRHNVTLAN--LRGVAKRW---------VIDHEREVQVA 388

Query: 144 EDARAG-------------DLSVEARQLVEIARALSYGARFIILDEPTAQLDGDEIKRLF 190
           E+ R               +LS   +Q V +++ L    + +ILDEPT  +D      ++
Sbjct: 389 EEFRRRLRIRCADVFQETVNLSGGNQQKVVLSKWLFADPQVLILDEPTRGIDVGAKYEIY 448

Query: 191 RRISELQREGVTFLFISHHLQEVYEICQAVTVLRDARHIVSAPVSALPREQLIEAM 246
             I++L  EG   + IS  + E+  +   + V+     +   P +   +E+++ A+
Sbjct: 449 TIINQLVAEGRGVVLISSEMPELLGVADRIYVMNAGEMVAEMPAAEASQEKIMGAI 504


Lambda     K      H
   0.318    0.134    0.377 

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: 623
Number of extensions: 31
Number of successful extensions: 10
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: 510
Length of database: 518
Length adjustment: 35
Effective length of query: 475
Effective length of database: 483
Effective search space:   229425
Effective search space used:   229425
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: 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
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