GapMind for catabolism of small carbon sources

 

Alignments for a candidate for thuK in Azospirillum brasilense Sp245

Align ABC transporter (characterized, see rationale)
to candidate AZOBR_RS25335 AZOBR_RS25335 putative ABC transporter (ATP-binding protein)

Query= uniprot:A0A166QFW2
         (381 letters)



>FitnessBrowser__azobra:AZOBR_RS25335
          Length = 365

 Score =  252 bits (643), Expect = 1e-71
 Identities = 143/320 (44%), Positives = 198/320 (61%), Gaps = 13/320 (4%)

Query: 1   MIKLKLDNVNKQLG-GMRILRDVSLEIAAGEFVVFVGPSGCGKSTLLRLIAGLDSICGGD 59
           ++ L LD + K+ G     L  +SLE+A GE +  VGPSGCGK+T LRLIAGL    GG 
Sbjct: 7   LVPLALDRLAKRYGTAPPALAALSLEVAGGELLGLVGPSGCGKTTALRLIAGLTPASGGR 66

Query: 60  LLIDGRRVNDLEPRERGVGMVFQSYALYPHMSVYDNISFGLKLAKTDKTSLRERVLKTAQ 119
           +L+ GR +  L    RG+G+VFQ+YAL+PHM+  DN++FGL++          R  +   
Sbjct: 67  VLVGGRDITALPAHARGIGLVFQNYALFPHMTAADNVAFGLRMRGLPAAERHARTAEALA 126

Query: 120 ILQLDKLLQRKPKELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIARL 179
           +++L  L  RKP+ LSGGQ+QRVA+ RA+A  P++LL DEPLSNLDA LR ++  EI  L
Sbjct: 127 MVRLSHLGGRKPRALSGGQQQRVALARALAIRPNLLLLDEPLSNLDAGLRAELLAEIRTL 186

Query: 180 HDRLGSTMIYVTHDQVEAMTLADKIVVLNGGRVEQVGSPRELYERPASRFVAGFLGSPRM 239
             RLG T ++VTHDQ EA+ + D+I VL  GR+EQVG+PRE+++RPAS FVAGF+G  R 
Sbjct: 187 QRRLGITALFVTHDQGEALAVCDRIAVLRDGRLEQVGTPREVHDRPASGFVAGFVG--RT 244

Query: 240 NFLSARLQTPGETSLVDTLVWGITSLPFDSSNLAAGTPLSLGIRPEHVSLKAADGTAGV- 298
           N + A     G   +  TL+  +   P       AG P+ L +RP  + + AA G  G+ 
Sbjct: 245 NRIPAERLAGGALRVGGTLLPALADGP-------AG-PVDLFVRPHRIRVGAAGGAGGLP 296

Query: 299 -VVTAVEYLGSETYVHLETG 317
            V+    +LG    + LE G
Sbjct: 297 AVLRGTAFLGDRIALSLEAG 316


Lambda     K      H
   0.320    0.137    0.394 

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: 402
Number of extensions: 12
Number of successful extensions: 1
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: 381
Length of database: 365
Length adjustment: 30
Effective length of query: 351
Effective length of database: 335
Effective search space:   117585
Effective search space used:   117585
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: 50 (23.9 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