GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braD in Dechlorosoma suillum PS

Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate Dsui_0629 Dsui_0629 branched-chain amino acid ABC-type transport system, permease component

Query= uniprot:Q1MCU0
         (300 letters)



>FitnessBrowser__PS:Dsui_0629
          Length = 307

 Score =  261 bits (667), Expect = 1e-74
 Identities = 143/308 (46%), Positives = 204/308 (66%), Gaps = 11/308 (3%)

Query: 1   MEYFVQQLLNGLTLGSIYGLVAIGYTMVYGIIGMINFAHGDIFMLGGFAALIVFLVLTSI 60
           M+ F+QQ++NGL LGSIY LVA+GYTMVYGI+G+INFAHG++ M+G   AL V  +L   
Sbjct: 1   MDIFLQQIINGLVLGSIYALVALGYTMVYGILGLINFAHGEVVMIGALTALTVVKLLAG- 59

Query: 61  FAGLPVAVLLLVMLVVAMLMTSLWNWTIERVAYRPLRGSFRLAPLITAIGMSITLSNFIQ 120
            +GLP  V+ L+ L+ A  +     + IE++AYRPLR + RLAPLITAIG+SI L N   
Sbjct: 60  -SGLPGPVIALIGLMAAAPVCMAIGYGIEKIAYRPLRKAPRLAPLITAIGVSIVLQNLAM 118

Query: 121 VTQGPRNKPIPPMV-SSVYQFGNISVSLKQIIIIVITAVLLTIFWYIVNRTALGRAQRAT 179
           +  G      P ++ +  ++    + +  Q+II+++ A ++     ++NRT LGRA RAT
Sbjct: 119 MVWGRSYHSFPAVLPAEAHEVLGATFTDLQVIIVLVAAGMMAGLLLLINRTRLGRAMRAT 178

Query: 180 EQDRKMAALLGVNVDQTISITFVMGAALAAVAGTMYLMYYGVASFNDGFTPGVKAFTAAV 239
            ++  +A L+GVNV+  IS+TFV+G+ALAAVAG M    Y +A +  GF  G+KAFTAAV
Sbjct: 179 AENPAIAQLMGVNVNHIISLTFVIGSALAAVAGLMVSANYSIAHYYMGFILGLKAFTAAV 238

Query: 240 LGGIGSLPGAVFGGLLIGLIESLWSAY--------FTIAYKDVATFAILAFVLIFKPTGI 291
           LGGIG+L GA+ GG+L+GLIESL + Y            Y+DV  F +L  VL+F+P+G+
Sbjct: 239 LGGIGNLAGAMIGGILLGLIESLGAGYIGDITGGFLGSHYQDVFAFFVLILVLVFRPSGL 298

Query: 292 LGRPEVEK 299
           +G    E+
Sbjct: 299 VGEKVAER 306


Lambda     K      H
   0.329    0.143    0.421 

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: 380
Number of extensions: 21
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: 300
Length of database: 307
Length adjustment: 27
Effective length of query: 273
Effective length of database: 280
Effective search space:    76440
Effective search space used:    76440
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: 48 (23.1 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