GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braD in Desulfovibrio vulgaris Miyazaki F

Align High-affinity branched-chain amino acid transport system permease protein BraD, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)
to candidate 8500415 DvMF_1165 inner-membrane translocator (RefSeq)

Query= TCDB::P21627
         (307 letters)



>FitnessBrowser__Miya:8500415
          Length = 306

 Score =  210 bits (535), Expect = 3e-59
 Identities = 115/308 (37%), Positives = 189/308 (61%), Gaps = 12/308 (3%)

Query: 7   YLQQLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYIAFIAITLLA--MMG 64
           ++Q L N L  GS YALIA+GYT+VYG++ +INFAHG+++M+G+YIAF   +LL   ++G
Sbjct: 4   FIQNLFNALQWGSFYALIALGYTLVYGVLLLINFAHGDIFMVGAYIAFFVSSLLLGDLLG 63

Query: 65  LDSVPLMMLAAFAA--SIIVTSAFGYSIERVAYRPLR--GGNRLIPLISAIGMSIFLQNA 120
           + ++P     A     ++++T+  G ++ER+AYRPLR  G +RL  +I+A+   + L+N 
Sbjct: 64  VFNLPGWAALALTVPLTMLLTAGVGVTLERIAYRPLRRKGAHRLYVVITALMCGLILENG 123

Query: 121 VMLSQDSKEKAIPTLLPGN-FVFGESSMNGVVISYMQILIFVVTFLVMFGLTLFISRSRL 179
            +    +  + +P ++    + FG  S     ++ +++ + +  FLV F L   ++R+R+
Sbjct: 124 NLALLGASRRKLPDMVDKVVYTFGSVS-----VTNLKVWVIITAFLVFFLLQFIVTRTRI 178

Query: 180 GRACRACAEDLKMTNLLGINSNNIIALTFVIGAALAAVAAVLLGMQYGVINPGIGFLAGI 239
           G A RA A D     L+GI  ++II  TFV+G+  A +A +L  M Y +++P +G + G 
Sbjct: 179 GMAMRAVAWDKFALPLMGIPLDSIIVFTFVLGSGFAGLAGLLFAMSYPILDPYMGAMVGW 238

Query: 240 KAFTAAVLGGIGSIPGAMLGGLLLGVAEAFGADVFGDQYKDVVAFGLLILVLLFRPTGIL 299
           KAF AAV+GGIG I GA +GG LL   E   A      ++D+ AF +L+++L  RPTG+ 
Sbjct: 239 KAFIAAVVGGIGDIRGAFIGGFLLAFIEIMVAAFLPSTFRDLFAFTILLMILWQRPTGLF 298

Query: 300 GRPEVEKV 307
           G  +  K+
Sbjct: 299 GVAKTTKI 306


Lambda     K      H
   0.328    0.145    0.413 

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: 280
Number of extensions: 14
Number of successful extensions: 3
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: 307
Length of database: 306
Length adjustment: 27
Effective length of query: 280
Effective length of database: 279
Effective search space:    78120
Effective search space used:    78120
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 48 (23.1 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