GapMind for catabolism of small carbon sources

 

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

Align glutamate-aspartate periplasmic-binding protein (characterized)
to candidate H281DRAFT_02625 H281DRAFT_02625 amino acid ABC transporter substrate-binding protein, PAAT family

Query= CharProtDB::CH_002441
         (302 letters)



>FitnessBrowser__Burk376:H281DRAFT_02625
          Length = 301

 Score =  341 bits (874), Expect = 1e-98
 Identities = 170/294 (57%), Positives = 207/294 (70%), Gaps = 4/294 (1%)

Query: 7   ATAILALALSAGLAQADDAAPAAGSTLDKIAKNGVIVVGHRESSVPFSYYDNQQKVVGYS 66
           A A+  L+L  G +    + P    TL KI    +I VGHRE+SVPFSY D    VVG+S
Sbjct: 10  AFALATLSLVTGTSYGQGSQP----TLAKIESTNLIAVGHRETSVPFSYVDTNNNVVGFS 65

Query: 67  QDYSNAIVEAVKKKLNKPDLQVKLIPITSQNRIPLLQNGTFDFECGSTTNNVERQKQAAF 126
           QD  N +++AVK K   PDL+V+ IP+TSQNRIPL+QNGT D ECG TTN   RQ Q AF
Sbjct: 66  QDLCNKVIDAVKLKTKHPDLRVRFIPVTSQNRIPLVQNGTIDLECGVTTNLTARQNQVAF 125

Query: 127 SDTIFVVGTRLLTKKGGDIKDFANLKDKAVVVTSGTTSEVLLNKLNEEQKMNMRIISAKD 186
           SDT FV  TRLLT+K   IKDF +L  K VV   GTTSE +L K+NEE+KMNM IISAKD
Sbjct: 126 SDTFFVATTRLLTRKDSGIKDFPDLAGKTVVTNQGTTSERILRKMNEEKKMNMSIISAKD 185

Query: 187 HGDSFRTLESGRAVAFMMDDALLAGERAKAKKPDNWEIVGKPQSQEAYGCMLRKDDPQFK 246
           +G+   TLE+GRAVA+MMDD LLAG R+   KP +W +VG PQS EAYG M+RKDDP+FK
Sbjct: 186 YGEGRATLETGRAVAYMMDDVLLAGTRSLTAKPSDWALVGTPQSSEAYGFMMRKDDPEFK 245

Query: 247 KLMDDTIAQVQTSGEAEKWFDKWFKNPIPPKNLNMNFELSDEMKALFKEPNDKA 300
           KL+DD ++QV  S E +  +DKWF  P+PPKN+N  F +S  M+ LF EPNDKA
Sbjct: 246 KLVDDAMSQVMRSPEIKTLYDKWFTKPVPPKNINFEFPMSGTMQKLFAEPNDKA 299


Lambda     K      H
   0.314    0.130    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: 290
Number of extensions: 8
Number of successful extensions: 1
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: 302
Length of database: 301
Length adjustment: 27
Effective length of query: 275
Effective length of database: 274
Effective search space:    75350
Effective search space used:    75350
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 (22.0 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