GapMind for catabolism of small carbon sources

 

Aligments for a candidate for leuT in Desulfovibrio vulgaris Miyazaki F

Align The amino acid (leucine):2 Na+ symporter, LeuTAa (Yamashita et al., 2005). LeuT possesses two ion binding sites, NA1 and NA2, both highly specific for Na+ but with differing mechanisms of binding (Noskov and Roux, 2008). X-ray structures have been determined for LeuT in substrate-free outward-open and apo inward-open states (characterized)
to candidate 8500111 DvMF_0874 sodium:neurotransmitter symporter (RefSeq)

Query= TCDB::O67854
         (513 letters)



>lcl|FitnessBrowser__Miya:8500111 DvMF_0874 sodium:neurotransmitter
           symporter (RefSeq)
          Length = 454

 Score =  193 bits (491), Expect = 1e-53
 Identities = 147/475 (30%), Positives = 240/475 (50%), Gaps = 49/475 (10%)

Query: 5   REHWATRLGLILAMAGNAVGLGNFLRFPVQAAENGGGAFMIPYIIAFLLVGIPLMWIEWA 64
           R+ +ATRLG++ A  G+AVGLGN  +FP    +NGG +F++ Y++A LLVG+P+M  E  
Sbjct: 9   RDGFATRLGVLAATLGSAVGLGNIWKFPALTGQNGGASFLLVYVLATLLVGLPVMISEIM 68

Query: 65  MGRYGGAQGHGTTPAIFYLLWRNRFAKILGVFGLWIPLVVAIYYVYIESWTLGFAIKFLV 124
           +GR   A   GT      L  + +   ++G  G+    ++  +Y  +  W   +  K L 
Sbjct: 69  LGRRARANAVGT---FRQLAPKGQPWHLVGFSGVVAAFLIMGFYTDVAGWVFAYIFKSLS 125

Query: 125 GLVPEPPPNATDPDSILRPFKEFLYSYIGVPKGDEPILKPSLFAYIVFLITMFINVSILI 184
           G +       TDP    + F+    + +G P      ++  L+ + V ++   I+V I+I
Sbjct: 126 GEIA-----TTDPAVAAKAFE----ALVGDP------VQSLLWQWGVLVL---ISV-III 166

Query: 185 RGISKGIERFAKIAMPTLFILAVFLVIRVFLLETPNGTAADGLNFLWTPDFEKLKDPGVW 244
            G+++GIER  K+ MP L +L V +  R   L      AA+GL FL+TPDF K+  PGV 
Sbjct: 167 AGVAQGIERTTKVLMPVLLLLLVAVCARSLTLP----KAAEGLAFLFTPDFSKI-TPGVI 221

Query: 245 IAAVGQIFFTLSLGFGAIITYASYVRKDQDIVLSGLTAATLNEKAEVILGGSISIPAAVA 304
           + A+G  FF LS+G G + TY SY R DQDI L+  T   L +    IL G    PA   
Sbjct: 222 LMALGLAFFKLSIGMGTMTTYGSYFRNDQDIPLTA-TRVMLCDLTISILAGMAVFPAVFN 280

Query: 305 FFGVANAVAIAKAGAFNLGFITLPAIFSQTAGGTFLGFLWFFLLFFAGLTSSIAIMQPMI 364
           F           +   +L F+T+PA+F+   GG     ++F L   A   + +++++  +
Sbjct: 281 F-------GFEPSAGPSLLFMTIPAVFTSLPGGQVFMVIFFCLTAIAATGAMLSLLEVPV 333

Query: 365 AFLEDELKLSRKHAVLWTA---AIVFFSAHLVM--------FLNKSLDEMDFWAGTIGVV 413
           A+L +   + RK A + T+   AI+   A L M        F     D  DF +  + + 
Sbjct: 334 AWLAESFGMPRKRATILTSVTLAIIGLPATLSMSTMANVKIFGMTVFDLYDFLSSNVLLP 393

Query: 414 FFGLTELIIFFWIFGADKAWEEI-NRGGIIKVPRI--YYYVMRYITPAFLAVLLV 465
             G+   +   W++GA     E+ NRG ++  P I  +  V+R+++P  + ++L+
Sbjct: 394 VGGIFICLFAGWVWGAANVKTELSNRGQLLNGPIIAAFLTVVRWVSPVLVLLVLL 448


Lambda     K      H
   0.330    0.146    0.463 

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: 619
Number of extensions: 34
Number of successful extensions: 5
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: 513
Length of database: 454
Length adjustment: 34
Effective length of query: 479
Effective length of database: 420
Effective search space:   201180
Effective search space used:   201180
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: 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:

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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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