GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_2396 in Desulfovibrio vulgaris Miyazaki F

Align Branched chain amino acid ABC transporter substrate-binding protein (characterized, see rationale)
to candidate 8502037 DvMF_2750 Extracellular ligand-binding receptor (RefSeq)

Query= uniprot:A0A165KTD4
         (375 letters)



>FitnessBrowser__Miya:8502037
          Length = 375

 Score =  151 bits (381), Expect = 3e-41
 Identities = 111/368 (30%), Positives = 166/368 (45%), Gaps = 8/368 (2%)

Query: 1   MQLKLKLTVVAAIAAAAGVASAQEQVVKIGHVAPVSGAQAHYGKDNENGARMAIEELNAQ 60
           M+  +K   +A  A+    A+A    VKIG + P++G  A  G+D  N   +  +ELN  
Sbjct: 1   MKHVVKALTLALAASLLMAATAFAAPVKIGLMCPLTGKWASEGQDMRNIVTLLADELNKA 60

Query: 61  GVTIGGKKIKFELVAEDDAADPKQGTAAAQKLCDAKVAGVVGHLNSGTTIPASKVYNDCG 120
           G  I G K+  ELV EDD  DP+    AAQKL  + V   +G   S  T  +  +Y++ G
Sbjct: 61  G-GINGNKV--ELVVEDDGGDPRTAALAAQKLTTSGVIAAIGTYGSAVTEASQSIYDEAG 117

Query: 121 IPHVTGAATNPNLTKPGYKTTFRIIANDNALGAGLAFYAVDTLKLKTVAIIDDRTAYGQG 180
           +  +   +T   LT+ G K   R    D+  G  +A   +     K VA++ D ++Y +G
Sbjct: 118 VVQIATGSTAVRLTEKGLKRFLRTAPRDDEQGM-VAAKLIKAKGYKAVALLHDNSSYAKG 176

Query: 181 VADVFKKTATAKGMKVVDEQFTTDKATDFMAILTAIKAKNPDAIFYGGMDPQGGPMLRQM 240
           +AD  K      G K+V     T    D+ AILT +KA NPD IF  G  P+ G +LRQ 
Sbjct: 177 LADETKALLDKAGTKIVFYDALTPGERDYTAILTKLKAANPDIIFCTGYYPEVGMLLRQK 236

Query: 241 EQLGMGNVKYFGGDGICTSEIAKLAAGAKTLGNVICAEGGSSLAKMPGGTAWKAKYDAKY 300
            ++   NV   GGD    +++ K++      G    +  G      P   +    Y AKY
Sbjct: 237 MEM-KWNVPMMGGDAANHADLVKISGKEAAKGYFFLSPPGPQDLDAPAAKSMLTAYKAKY 295

Query: 301 PN-QFQVYSPYTYDATFLIVDAMKRANSVDPKVYTPELAK--SSFKGVTSTIAFEPNGEM 357
                 V+S    DA  +IV+A+K     D       L     ++ G T  I+F   G+ 
Sbjct: 296 NGVPGSVWSVLAGDAFNVIVEAVKSTGKADSGAIAEYLKTKLKNYPGFTGQISFNEKGDR 355

Query: 358 KNPAITLY 365
                 +Y
Sbjct: 356 VGDLYRVY 363


Lambda     K      H
   0.315    0.131    0.375 

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: 336
Number of extensions: 15
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: 375
Length of database: 375
Length adjustment: 30
Effective length of query: 345
Effective length of database: 345
Effective search space:   119025
Effective search space used:   119025
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 50 (23.9 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