GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livJ in Paraburkholderia bryophila 376MFSha3.1

Align Branched chain amino acid ABC transporter substrate-binding protein (characterized, see rationale)
to candidate H281DRAFT_02405 H281DRAFT_02405 amino acid/amide ABC transporter substrate-binding protein, HAAT family

Query= uniprot:A0A165KTD4
         (375 letters)



>FitnessBrowser__Burk376:H281DRAFT_02405
          Length = 382

 Score =  332 bits (851), Expect = 1e-95
 Identities = 178/380 (46%), Positives = 241/380 (63%), Gaps = 9/380 (2%)

Query: 1   MQLKLKLTVVAAIAAA---AGVASAQE-QVVKIGHVAPVSGAQAHYGKDNENGARMAIEE 56
           MQ K+     AA+ AA   AG A+AQ    VKIG   P++GAQAHYGKD +NG  +A+E+
Sbjct: 1   MQHKMTQLAGAALVAAMSLAGTANAQSTDDVKIGFAGPMTGAQAHYGKDFQNGITLAVED 60

Query: 57  LNAQGVTIGGKKIKFELVAEDDAADPKQGTAAAQKLCDAKVAGVVGHLNSGTTIPASKVY 116
           +NA    IGGK ++F L + DD ADP+ GT  AQKL D  + G++GH NSGTTIPAS++Y
Sbjct: 61  INATKPVIGGKPVRFVLDSADDQADPRTGTTVAQKLVDDGIKGMLGHFNSGTTIPASRIY 120

Query: 117 NDCGIPHVTGAATNPNLTKPGYKTTFRIIANDNALGAGLAFYAVDTLKLKTVAIIDDRTA 176
            + GIP +   AT P  T+ G+KTTFR++ +D   G+    +AV TL +K + I+DDRTA
Sbjct: 121 ANAGIPEIA-MATAPEYTQQGFKTTFRMMTSDTQQGSVAGTFAVKTLGVKKIVIVDDRTA 179

Query: 177 YGQGVADVFKKTATAKGMKVVDEQFTTDKATDFMAILTAIKAKNPDAIFYGGMDPQGGPM 236
           YGQG+AD F+K A A G  +VD ++T DKA DF +ILT +KA NPD I+YGG D Q  PM
Sbjct: 180 YGQGLADQFEKAAKAAGGTIVDREYTNDKAVDFKSILTKLKAANPDLIYYGGADSQAAPM 239

Query: 237 LRQMEQLGMGNVKYFGGDGICTSEIAKLAAGAKTLGNVICAEGGSSLAKMPGGTAWKAKY 296
           ++QM+ LG+      GG+ + T    ++A  A      + +  G  L +MPGG  + AKY
Sbjct: 240 VKQMKALGI-KAPLMGGEMVHTPTFIQIAGDA--ANGTVASLAGLPLEEMPGGKDYVAKY 296

Query: 297 DAKYPNQFQVYSPYTYDATFLIVDAMKRANSVDPKVYTPELAKSSFKGVTST-IAFEPNG 355
             ++    Q YSPY YD    +  AMK+ANS DP  Y P LAK+S   VTS+ ++++  G
Sbjct: 297 KKRFNEDVQTYSPYAYDGAMAMFAAMKKANSTDPAKYLPVLAKTSMPAVTSSNLSYDAKG 356

Query: 356 EMKNPAITLYVYKDGKKTPL 375
           ++KN  ITLY   DGK T L
Sbjct: 357 DLKNGGITLYKVVDGKWTTL 376


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: 499
Number of extensions: 25
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: 375
Length of database: 382
Length adjustment: 30
Effective length of query: 345
Effective length of database: 352
Effective search space:   121440
Effective search space used:   121440
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.

Links

Downloads

Related tools

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