GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livM in Desulfovibrio vulgaris Miyazaki F

Align High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)
to candidate 8502039 DvMF_2752 inner-membrane translocator (RefSeq)

Query= TCDB::P21628
         (417 letters)



>FitnessBrowser__Miya:8502039
          Length = 330

 Score =  214 bits (545), Expect = 3e-60
 Identities = 131/325 (40%), Positives = 186/325 (57%), Gaps = 27/325 (8%)

Query: 85  LSLPSTQRWAVLALVVVAFVWPFFASRGAVDIATLILIYVMLGIGLNIVVGLAGLLDLGY 144
           +++  T  +A +A+VV   V P        D+   I +Y +L + LNI++G AGL  +G+
Sbjct: 1   MTVSRTTSYAGIAVVVA--VLPLLLDPYWTDVFVSIGLYSVLALSLNIILGQAGLFHMGH 58

Query: 145 VGFYAVGAYTYALLAEYAGFGFWTALPIAGMMAALFGFLLGFPVLRLRGDYLAIVTLGFG 204
             FYAVGAY  A+     G     A+P AG+ AALF  ++  P++ LRGDYL IVT+G  
Sbjct: 59  AAFYAVGAYVTAIANTMWGVPVLWAMPFAGLAAALFAMVVARPIIHLRGDYLLIVTIGIV 118

Query: 205 EIIRI-LLRNMTEITGGPNGIGSIPKPTLFGLTFERRAPEGMQTFHEFFGIAYNTNYKVI 263
           EI+RI L+ N+  +TGG NGI  I +P LFG                 F IA     K +
Sbjct: 119 EIVRIALINNVFGLTGGANGIFGISRPMLFG-----------------FKIA-----KPV 156

Query: 264 LLYVVALLLVLLALFVINRLMRMPIGRAWEALREDEVACRALGLNPTIVKLSAFTIGASF 323
             Y +    V  ++ +  RL     GRA   ++ED+ A    G+N    KL AF +GA +
Sbjct: 157 HFYYLVWAYVACSILLFRRLENSRFGRALNYIKEDDTAAEGSGVNIASYKLWAFVLGAFW 216

Query: 324 AGFAGSFFAARQGLVTPESFTFIESAMILAIVVLGGMGSQLGVILAAVVMVLLQEM-RGF 382
           AG  G+ +AA+  +++PESF+F ES ++ AIV+LGG GS  GV+L A +++ L E  R F
Sbjct: 217 AGMTGTIYAAKMTIISPESFSFWESVVLFAIVILGG-GSNRGVLLGAFLLIGLPEFFREF 275

Query: 383 NEYRMLIFGLTMIVMMIWRPQGLLP 407
              RML FGL M+VMMI+RPQG+LP
Sbjct: 276 ASARMLAFGLAMVVMMIFRPQGMLP 300


Lambda     K      H
   0.330    0.146    0.439 

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: 436
Number of extensions: 25
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: 417
Length of database: 330
Length adjustment: 30
Effective length of query: 387
Effective length of database: 300
Effective search space:   116100
Effective search space used:   116100
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 49 (23.5 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