GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braD in Desulfovibrio vulgaris Miyazaki F

Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate 8500415 DvMF_1165 inner-membrane translocator (RefSeq)

Query= uniprot:Q1MCU0
         (300 letters)



>FitnessBrowser__Miya:8500415
          Length = 306

 Score =  211 bits (538), Expect = 1e-59
 Identities = 119/306 (38%), Positives = 178/306 (58%), Gaps = 6/306 (1%)

Query: 1   MEYFVQQLLNGLTLGSIYGLVAIGYTMVYGIIGMINFAHGDIFMLGGFAALIVFLVLTSI 60
           ME F+Q L N L  GS Y L+A+GYT+VYG++ +INFAHGDIFM+G + A  V  +L   
Sbjct: 1   MEIFIQNLFNALQWGSFYALIALGYTLVYGVLLLINFAHGDIFMVGAYIAFFVSSLLLGD 60

Query: 61  FAG---LPVAVLLLVMLVVAMLMTSLWNWTIERVAYRPLR--GSFRLAPLITAIGMSITL 115
             G   LP    L + + + ML+T+    T+ER+AYRPLR  G+ RL  +ITA+   + L
Sbjct: 61  LLGVFNLPGWAALALTVPLTMLLTAGVGVTLERIAYRPLRRKGAHRLYVVITALMCGLIL 120

Query: 116 SNFIQVTQGPRNKPIPPMVSSV-YQFGNISVSLKQIIIIVITAVLLTIFWYIVNRTALGR 174
            N      G   + +P MV  V Y FG++SV+  ++ +I+   ++  +  +IV RT +G 
Sbjct: 121 ENGNLALLGASRRKLPDMVDKVVYTFGSVSVTNLKVWVIITAFLVFFLLQFIVTRTRIGM 180

Query: 175 AQRATEQDRKMAALLGVNVDQTISITFVMGAALAAVAGTMYLMYYGVASFNDGFTPGVKA 234
           A RA   D+    L+G+ +D  I  TFV+G+  A +AG ++ M Y +     G   G KA
Sbjct: 181 AMRAVAWDKFALPLMGIPLDSIIVFTFVLGSGFAGLAGLLFAMSYPILDPYMGAMVGWKA 240

Query: 235 FTAAVLGGIGSLPGAVFGGLLIGLIESLWSAYFTIAYKDVATFAILAFVLIFKPTGILGR 294
           F AAV+GGIG + GA  GG L+  IE + +A+    ++D+  F IL  +L  +PTG+ G 
Sbjct: 241 FIAAVVGGIGDIRGAFIGGFLLAFIEIMVAAFLPSTFRDLFAFTILLMILWQRPTGLFGV 300

Query: 295 PEVEKV 300
            +  K+
Sbjct: 301 AKTTKI 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: 302
Number of extensions: 12
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: 300
Length of database: 306
Length adjustment: 27
Effective length of query: 273
Effective length of database: 279
Effective search space:    76167
Effective search space used:    76167
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