GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braD in Marinobacter adhaerens HP15

Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate GFF3113 HP15_3056 high-affinity branched-chain amino acid ABC transporter, permease protein

Query= uniprot:Q1MCU0
         (300 letters)



>FitnessBrowser__Marino:GFF3113
          Length = 307

 Score =  313 bits (803), Expect = 2e-90
 Identities = 162/304 (53%), Positives = 218/304 (71%), Gaps = 8/304 (2%)

Query: 3   YFVQQLLNGLTLGSIYGLVAIGYTMVYGIIGMINFAHGDIFMLGGFAALIVFLVLTSI-F 61
           YF QQL+NGLT+GS Y L+AIGYTMVYGIIGMINFAHG+I+M+G + ALI    L ++  
Sbjct: 6   YFSQQLINGLTIGSTYALIAIGYTMVYGIIGMINFAHGEIYMIGAYTALIAITGLAALGI 65

Query: 62  AGLPVAVLLLVMLVVAMLMTSLWNWTIERVAYRPLRGSFRLAPLITAIGMSITLSNFIQV 121
           A LP+  +L+V L+ AM+++S   W +ERVAYRP+RG  RL PLI+AIGMSI L N++ +
Sbjct: 66  AWLPL--ILIVALLCAMIVSSSMGWAVERVAYRPVRGRHRLIPLISAIGMSIFLQNYVHL 123

Query: 122 TQGPRNKPIPPMVSSVYQFGN-----ISVSLKQIIIIVITAVLLTIFWYIVNRTALGRAQ 176
            QG RN   P ++   + FG+     +S+S  QI I + T + +T     ++R+  GRA 
Sbjct: 124 AQGSRNIGFPALIDGGFNFGSGDGFQMSLSYMQITIFITTLICMTALSLFISRSRTGRAC 183

Query: 177 RATEQDRKMAALLGVNVDQTISITFVMGAALAAVAGTMYLMYYGVASFNDGFTPGVKAFT 236
           RA  QD  MA LLG++ ++ IS TFV+GAALAAVAG +  MYYG      GF  G+KAFT
Sbjct: 184 RAVSQDLGMANLLGIDTNRIISATFVIGAALAAVAGLLLGMYYGSVDPLFGFIAGLKAFT 243

Query: 237 AAVLGGIGSLPGAVFGGLLIGLIESLWSAYFTIAYKDVATFAILAFVLIFKPTGILGRPE 296
           AAVLGGIGS+PGA+ GGL++G+ ES+ S Y +  YKDV +F++L  +L+FKPTG+LG+PE
Sbjct: 244 AAVLGGIGSIPGAMLGGLILGVAESMTSGYLSGEYKDVISFSLLILILLFKPTGLLGKPE 303

Query: 297 VEKV 300
           VEK+
Sbjct: 304 VEKI 307


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: 353
Number of extensions: 18
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: 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