GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braD in Dinoroseobacter shibae DFL-12

Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate 3607448 Dshi_0861 inner-membrane translocator (RefSeq)

Query= uniprot:Q1MCU0
         (300 letters)



>FitnessBrowser__Dino:3607448
          Length = 305

 Score =  130 bits (328), Expect = 3e-35
 Identities = 98/310 (31%), Positives = 152/310 (49%), Gaps = 32/310 (10%)

Query: 5   VQQLLNGLTLGSIYGLVAIGYTMVYGIIGMINFAHGDIFMLGGFAALIVFLVLTSIFAGL 64
           ++Q+LNGL  G +  L+A G T+V+G++G+IN AHG ++M+G FAA  V     S   GL
Sbjct: 7   IEQVLNGLQFGVMLFLMAAGLTLVFGVMGLINLAHGSLYMVGAFAAAAVAGATGSFVLGL 66

Query: 65  PVAVLLLVMLVVAMLMTSLWNWTIERVAYRPLRGSFRLAPLITAIGMSITLSNFIQVTQG 124
             A      L  A    +L    IE    R L     L  ++    + +  S   +   G
Sbjct: 67  AAA------LAAAAAAGAL----IEVTIIRRLYARDHLDQVLATFALILIFSEGTRWIFG 116

Query: 125 --PRNKPIPPMVSS--VYQFGNISVSLKQIIIIVITAVLLTIFWYIVNRTALGRAQRATE 180
             P    +P  +S      FG    + +  II +  A+   +FW ++ +T +G   RA E
Sbjct: 117 SFPLFLEVPAALSGPVTLPFGIEYPAYRLAIIGIGLAIAAALFW-LIAKTRIGVQIRAGE 175

Query: 181 QDRKMAALLGVNVDQTISITFVMGAALAAVAGTMYLMYYGVASFNDGFTPGVKAFTAAVL 240
            DR+M A LGV++D+  ++ F +GAALA +AG +      V     G    + AF   V+
Sbjct: 176 ADREMIAALGVDIDRLYTLVFALGAALAGLAGALVGALQSV-QVGMGEPVLILAFVVIVI 234

Query: 241 GGIGSLPGAVFGGLLIGLIESLWSAYFTIAYKDV----------------ATFAILAFVL 284
           GGIGS+ GA  G LL+GL ++L      +A+  V                A + ++A VL
Sbjct: 235 GGIGSIKGAFVGALLLGLTDTLGRTLLPVAFGTVLEPSMATAVGSALASMAIYILMAGVL 294

Query: 285 IFKPTGILGR 294
           IF+P+G+ G+
Sbjct: 295 IFRPSGLFGQ 304


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: 294
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: 300
Length of database: 305
Length adjustment: 27
Effective length of query: 273
Effective length of database: 278
Effective search space:    75894
Effective search space used:    75894
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