GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braE in Lutibaculum baratangense AMV1

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 WP_023434295.1 N177_RS20200 high-affinity branched-chain amino acid ABC transporter permease LivM

Query= TCDB::P21628
         (417 letters)



>NCBI__GCF_000496075.1:WP_023434295.1
          Length = 441

 Score =  409 bits (1051), Expect = e-119
 Identities = 218/419 (52%), Positives = 294/419 (70%), Gaps = 8/419 (1%)

Query: 2   SQSLKRALFSALLVILVSYPILGLKLRTV--GIKLEVLGADAQTLWTIAAAALAMFVWQL 59
           ++ +K A +SAL+ + ++ PI+GL+  T   G+ L     D   +     A   +  + +
Sbjct: 12  AELVKDAAYSALIALALAAPIIGLQTVTARGGLGLNARWDDVFLIVLAVFAGRLLLNFTI 71

Query: 60  FRDRIPLKLGRGVGYKVNGSGL-KNFLSLPSTQRWAVLALVVVAFVWPFFASRGAVDIAT 118
           +R +    +G+    +  G    ++  +L        LA+ ++    PF + R  +D++ 
Sbjct: 72  WRHQGARPIGQKWFQRAGGRPFARHGHTLSKIIGPLALAVALLLPALPF-SDRYVMDLSI 130

Query: 119 LILIYVMLGIGLNIVVGLAGLLDLGYVGFYAVGAYTYALLAEYAGFGFWTALPIAGMMAA 178
           ++L Y+MLG GLNIVVGLAGLLDLGYV FYA+GAY++ALLA +   GFW  LP+AG++AA
Sbjct: 131 MVLTYIMLGWGLNIVVGLAGLLDLGYVAFYAIGAYSFALLATHFDLGFWICLPLAGILAA 190

Query: 179 LFGFLLGFPVLRLRGDYLAIVTLGFGEIIRILLRNMTEITGGPNGIGSIPKPTLFGLTFE 238
            +G +LGFPVLRLRGDYLAIVTL FGEIIR++L N  E TGGPNGI  IP PTLFGL F 
Sbjct: 191 FWGVILGFPVLRLRGDYLAIVTLAFGEIIRVVLLNWYEFTGGPNGILGIPDPTLFGLEFA 250

Query: 239 RRAPEGMQTFHEFFGIAYNTNYKVILLYVVALLLVLLALFVINRLMRMPIGRAWEALRED 298
           RR   G  TFHEFFG++Y++ +K+I LY + L L L+  FV  RL R+P+GRAWEALRED
Sbjct: 251 RR---GDNTFHEFFGLSYSSMHKIIFLYYIILCLALITNFVTLRLRRLPVGRAWEALRED 307

Query: 299 EVACRALGLNPTIVKLSAFTIGASFAGFAGSFFAARQGLVTPESFTFIESAMILAIVVLG 358
           E+ACR+LG+N T  KL+AF IGA F GFAGSFFA RQG ++PESFTFIESA+ILAIVVLG
Sbjct: 308 EIACRSLGINTTNTKLTAFAIGAMFGGFAGSFFATRQGFISPESFTFIESALILAIVVLG 367

Query: 359 GMGSQLGVILAAVVMV-LLQEMRGFNEYRMLIFGLTMIVMMIWRPQGLLPMQRPHLELK 416
           G+GSQ+GV++AA+VM+   +  R F +YRMLIFGL M+ +M+WRP+GL+  + P + LK
Sbjct: 368 GLGSQVGVVIAAIVMMGGFEYFREFEQYRMLIFGLAMVFIMVWRPRGLISTRSPSVILK 426


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: 592
Number of extensions: 33
Number of successful extensions: 4
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: 441
Length adjustment: 32
Effective length of query: 385
Effective length of database: 409
Effective search space:   157465
Effective search space used:   157465
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: 51 (24.3 bits)

This GapMind analysis is from Sep 24 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