GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AZOBR_RS08235 in Desulfovibrio vulgaris Hildenborough

Align L-proline and D-alanine ABC transporter, permease component 1 (characterized)
to candidate 208249 DVU2743 high-affinity branched-chain amino acid ABC ransporter, permease protein

Query= reanno::azobra:AZOBR_RS08235
         (301 letters)



>MicrobesOnline__882:208249
          Length = 306

 Score =  211 bits (537), Expect = 2e-59
 Identities = 119/308 (38%), Positives = 192/308 (62%), Gaps = 9/308 (2%)

Query: 1   MEYFLQQLINGLSLGAIYGLIAIGYTMVYGIIGMINFAHGEIYMIGAFVAL-ITFLAIGS 59
           ME F+Q + N L  G+ Y LIA+GYT+VYG++ +INFAHG+I+M+GA+++  +  + +G 
Sbjct: 1   METFIQNIFNALQWGSFYALIALGYTLVYGVLLLINFAHGDIFMVGAYISFFVASILLGQ 60

Query: 60  LGITWV---PLALLVMLVASMLFTAVYGWTVERIAYRPLR--SSPRLAPLISAIGMSIFL 114
           +G  +    P+AL + +  +M+ TA  G T+ER+AYRPLR   + RL  +I+A+   I L
Sbjct: 61  IGGFFELSGPMALALTVPLTMVLTAGVGVTLERVAYRPLRRKGAHRLYVVITALMCGIML 120

Query: 115 QNYVQILQGARSKPLQPILPGNLTLMDGAVSVSYVRLATIVITIALMYGFTQ-LITRTSL 173
           +N    L GA  K L P +   +    G VSV+ ++L  +++T  L++   Q ++TRT +
Sbjct: 121 ENGNLALLGASRKAL-PEMIDKVVYTIGTVSVTNLKLM-VIVTAFLVFALLQFIVTRTRI 178

Query: 174 GRAQRACEQDKKMAGLLGVNVDRVISLTFVMGAALAAVAGMMVLLIYGVIDFYIGFLAGV 233
           G A RA   DK    L+G+ +D +I  TFV+G+  A +AG++  + Y ++D Y+G + G 
Sbjct: 179 GMAMRAVAWDKFALPLMGIPLDSIIVFTFVLGSGFAGLAGLLFAMSYPILDPYMGAMVGW 238

Query: 234 KAFTAAVLGGIGSLPGAMLGGVVIGLIEAFWSGYMGSEWKDVATFTILVLVLIFRPTGLL 293
           KAF AAV+GGIG + GA +GG ++  IE   +    S ++D+  F+IL+ ++  RPTGL 
Sbjct: 239 KAFIAAVVGGIGDIRGAFIGGFLLAFIEIMVAAVFPSTFRDLFAFSILLFIMWQRPTGLF 298

Query: 294 GRPEIEKV 301
           G  +  K+
Sbjct: 299 GVAKTTKI 306


Lambda     K      H
   0.329    0.144    0.425 

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: 277
Number of extensions: 17
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: 301
Length of database: 306
Length adjustment: 27
Effective length of query: 274
Effective length of database: 279
Effective search space:    76446
Effective search space used:    76446
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