GapMind for catabolism of small carbon sources

 

Aligments for a candidate for AO353_21715 in Desulfovibrio vulgaris Miyazaki F

Align ABC transporter for D-Glucosamine, permease component 2 (characterized)
to candidate 8502448 DvMF_3154 polar amino acid ABC transporter, inner membrane subunit (RefSeq)

Query= reanno::pseudo5_N2C3_1:AO356_00475
         (220 letters)



>lcl|FitnessBrowser__Miya:8502448 DvMF_3154 polar amino acid ABC
           transporter, inner membrane subunit (RefSeq)
          Length = 229

 Score =  129 bits (324), Expect = 5e-35
 Identities = 87/226 (38%), Positives = 125/226 (55%), Gaps = 15/226 (6%)

Query: 5   LNFAAVWRDFDTLLAG------LGLGLSLALVSIAIGCVIG---LAMAFALL--SKHRVL 53
           + +  VWR+FD LL G      LG GL++++V +AIG + G   L + F LL  S    L
Sbjct: 1   MQWDVVWRNFDYLLVGSWPQGPLG-GLAMSVV-LAIGGIFGAFWLGLGFGLLRLSDRWWL 58

Query: 54  RVLASVYVTVIRNTPILVLILLIYFALPS-LGIRLDKLPSFVITLSLYAGAYLTEVFRGG 112
           R+ A +YV +IR  P+L+LI   YF  P  LG  L +  S ++   ++ GAY+ E+ R G
Sbjct: 59  RLPAIIYVEIIRGIPLLMLIFWFYFLAPIVLGRTLPEAESALVAFIVFTGAYIAEIVRAG 118

Query: 113 LLSIHKGQREAGLAIGLGEWQVKAYVTVPVMLRNVLPALSNNFISLFKDTSLAAAIAVPE 172
           +L++  GQ EA    GL + Q   YV +P  LRN++P+  N F+SL KDTSLA  I V E
Sbjct: 119 VLALPHGQMEAARGTGLSKSQAMIYVILPQALRNMIPSFVNQFVSLTKDTSLAYIIGVSE 178

Query: 173 LTYYARKI-NVESYRVIETWLVTTALYVAACYLIAMVLRYFEQRLA 217
           LT  A +I N E     E +     LY   C+ +    R  E+++A
Sbjct: 179 LTRTATQINNRELTAPAELFFTIAVLYFIVCWTLTAASRRMERQMA 224


Lambda     K      H
   0.329    0.142    0.414 

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: 141
Number of extensions: 10
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: 220
Length of database: 229
Length adjustment: 22
Effective length of query: 198
Effective length of database: 207
Effective search space:    40986
Effective search space used:    40986
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 (21.8 bits)
S2: 46 (22.3 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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