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_04062 H281DRAFT_04062 amino acid/amide ABC transporter membrane protein 1, HAAT family

Query= uniprot:Q1MCU0
         (300 letters)



>FitnessBrowser__Burk376:H281DRAFT_04062
          Length = 316

 Score =  259 bits (662), Expect = 6e-74
 Identities = 141/309 (45%), Positives = 200/309 (64%), Gaps = 16/309 (5%)

Query: 1   MEYFVQQLLNGLTLGSIYGLVAIGYTMVYGIIGMINFAHGDIFMLGGFAALIVFLVLTSI 60
           M+ F+QQ+LNGL LGS+Y ++A+GYTMVYGI+G+INFAHGD+ M+G   AL    VL + 
Sbjct: 1   MDIFIQQILNGLVLGSVYAIIALGYTMVYGILGIINFAHGDVLMVGAMVALSAIGVLQNH 60

Query: 61  FAGLPVAVLLLVMLVVAMLMTSLWNWTIERVAYRPLRGSFRLAPLITAIGMSITLSNFIQ 120
           F GL     L + L +A ++ ++  +TIERVAYRPLR + RLAPLITAIG+SI L     
Sbjct: 61  FPGLGNVPTLCIALAIAAVVCAVVGYTIERVAYRPLRKAPRLAPLITAIGVSILLQTLAM 120

Query: 121 VTQGPRNKPIPPM--------VSSVYQFGNISVSLKQIIIIVITAVLLTIFWYIVNRTAL 172
           +       P P +        + +        +S+ +I+IIV+  +++     +V++T L
Sbjct: 121 MIWSRNPLPFPQLLPTDPLNVIKATDTTPGAVISMTEIVIIVVAFLVMAGLLLLVHKTKL 180

Query: 173 GRAQRATEQDRKMAALLGVNVDQTISITFVMGAALAAVAGTMYLMYYGVASFNDGFTPGV 232
           GRA RA  ++  +A+L+GVN +  IS TF++G+ALAA+AG M    YG A F  GF PG+
Sbjct: 181 GRAMRAIAENPGVASLMGVNPNFVISATFMIGSALAALAGVMIASEYGNAHFYMGFIPGL 240

Query: 233 KAFTAAVLGGIGSLPGAVFGGLLIGLIESLWSAY--------FTIAYKDVATFAILAFVL 284
           KAFTAAVLGGIG+L GA+ GG+++GLIE L + Y        F   Y+DV  F +L  VL
Sbjct: 241 KAFTAAVLGGIGNLGGAMVGGVILGLIEQLGAGYIGNLTGGVFGSNYQDVFAFIVLIIVL 300

Query: 285 IFKPTGILG 293
           +F+P+G+LG
Sbjct: 301 VFRPSGLLG 309


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: 358
Number of extensions: 16
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: 316
Length adjustment: 27
Effective length of query: 273
Effective length of database: 289
Effective search space:    78897
Effective search space used:    78897
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