GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AZOBR_RS08260 in Pseudomonas fluorescens FW300-N2E3

Align Branched-chain amino acid ABC transporter,substrate-binding periplasmic component (characterized, see rationale)
to candidate AO353_13340 AO353_13340 amino acid ABC transporter substrate-binding protein

Query= uniprot:G8ALJ3
         (366 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_13340
          Length = 377

 Score =  337 bits (863), Expect = 4e-97
 Identities = 174/362 (48%), Positives = 241/362 (66%), Gaps = 4/362 (1%)

Query: 9   VAVAATAMTASVAKADIAVATAGPITGQYATFGEQMKKGIEQAVADINAAGGVLGQKLKL 68
           +AVAA    +S  +AD+ +  AGP+TG  A+FG Q  KG + A   INA GG+ G+K+ L
Sbjct: 13  LAVAAALGVSSFVQADVKLGVAGPMTGPSASFGLQYMKGAQAAADAINAKGGINGEKIVL 72

Query: 69  EVGDDACDPKQAVAVANQLAKAGVKFVAGHFCSGSSIPASQVYAEEGVLQISPASTNPKL 128
             GDDAC+PKQAVAVAN++ +  V  V GHFCS S+IPAS+VY++ G++ I+P STNP +
Sbjct: 73  VQGDDACEPKQAVAVANKMVQDKVIGVVGHFCSSSTIPASEVYSDAGIIAITPGSTNPTV 132

Query: 129 TEQNLKNVFRVCGRDDQQGQIAGKYLLENYKGKNVAILHDKSAYGKGLADETQKALNAGG 188
           TE+ L  + R+CGRDDQQG +AG Y+++  KGK VA+++DK  YGKGLAD T K L A G
Sbjct: 133 TERGLPAMMRMCGRDDQQGIVAGNYIVDVLKGKKVAVINDKDTYGKGLADATAKQLTARG 192

Query: 189 QKEKIYEAYTAGEKDYSALVSKLKQEAVDVVYVGGYHTEAGLLARQMKDQGL-NAPIVSG 247
            K  + E  T GEKD+SAL++K++    DV+Y GG H EAG L  Q+++QGL +   +S 
Sbjct: 193 VKPVLEEGLTRGEKDFSALITKVRSVGADVLYFGGLHPEAGPLVHQLREQGLKDVKFMSD 252

Query: 248 DALVTNEYWAITG--PAGENTMMTFGPDPREMPEAKEAVEKFRKAGYEPEGYTLYTYAAL 305
           D +VT+E     G  P  +   MTFG DPR +P++K  V+ FRK+GYEPEGYTLY YA++
Sbjct: 253 DGIVTDEMVTTAGGAPYVDGVYMTFGADPRLIPDSKAVVDTFRKSGYEPEGYTLYAYASV 312

Query: 306 QIWAEAAKQANSTDSAKIADVLRKNSYNTVIGKIGFDAKGDVTSPAYVWYRWN-NGQYAQ 364
           Q  A     A S    + A  L+ +   TV+GK  +D+KGD+    YV Y+W+  G+Y Q
Sbjct: 313 QALAAGFNGAKSNKGEEAAKWLKAHPVETVMGKKEWDSKGDLKISDYVVYQWDAAGKYHQ 372

Query: 365 VK 366
           ++
Sbjct: 373 LE 374


Lambda     K      H
   0.312    0.129    0.366 

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: 417
Number of extensions: 17
Number of successful extensions: 2
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: 366
Length of database: 377
Length adjustment: 30
Effective length of query: 336
Effective length of database: 347
Effective search space:   116592
Effective search space used:   116592
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 49 (23.5 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