GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braD in Paraburkholderia bryophila 376MFSha3.1

Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate H281DRAFT_00093 H281DRAFT_00093 amino acid/amide ABC transporter membrane protein 1, HAAT family

Query= uniprot:Q1MCU0
         (300 letters)



>FitnessBrowser__Burk376:H281DRAFT_00093
          Length = 551

 Score =  125 bits (313), Expect = 3e-33
 Identities = 85/287 (29%), Positives = 141/287 (49%), Gaps = 6/287 (2%)

Query: 8   LLNGLTLGSIYGLVAIGYTMVYGIIGMINFAHGDIFMLGGFAALIVFLVLTSIFAGLPVA 67
           L  GL+LGS+  L A+G  + YG+IG+IN AHG+  M+G +A  +V   L   FA     
Sbjct: 258 LFAGLSLGSVLLLAALGLAITYGLIGVINMAHGEFLMIGAYATYVV-QNLFQRFAPGGFD 316

Query: 68  VLLLVMLVVAMLMTSLWNWTIERVAYRPLRGSFRLAPLITAIGMSITLSNFIQVTQGPRN 127
              LV +  + +  +L    IER+  + L G   L  L+T  G+S+ L    ++  G +N
Sbjct: 317 WYPLVAVPASFVAAALVGIVIERLVLKHLYGR-PLETLLTTFGISLILIQATRMLFGAQN 375

Query: 128 KPIPP---MVSSVYQFGNISVSLKQIIIIVITAVLLTIFWYIVNRTALGRAQRATEQDRK 184
             +     M   V    N+ +   ++ I+  + +++ I W ++ +T LG   RA  Q+R+
Sbjct: 376 VQVVNPSWMSGGVTVMANLILPYNRLAILAFSLIVVGIAWAVLTKTRLGLFVRAVTQNRR 435

Query: 185 MAALLGVNVDQTISITFVMGAALAAVAGTMYLMYYGVASFNDGFTPGVKAFTAAVLGGIG 244
           MAA +GV   +  S  F  GA +A + G   L   G    + G +  + +F A VLGG+G
Sbjct: 436 MAACVGVKTARVDSYAFAFGAGIAGLGGCA-LSQIGNVGPDLGQSYIIDSFMAVVLGGVG 494

Query: 245 SLPGAVFGGLLIGLIESLWSAYFTIAYKDVATFAILAFVLIFKPTGI 291
            L G V GG  +GL+      ++      +A   ++   +  +P G+
Sbjct: 495 QLAGTVIGGFGLGLVSKAIEPFWGAVLAKIAVLVLIVLFIQKRPQGM 541


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: 369
Number of extensions: 21
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 300
Length of database: 551
Length adjustment: 31
Effective length of query: 269
Effective length of database: 520
Effective search space:   139880
Effective search space used:   139880
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: 50 (23.9 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