GapMind for catabolism of small carbon sources

 

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

Align ABC transporter for L-asparagine and L-glutamate, periplasmic substrate-binding component (characterized)
to candidate AO353_08055 AO353_08055 ABC transporter

Query= reanno::pseudo1_N1B4:Pf1N1B4_771
         (304 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_08055
          Length = 300

 Score =  350 bits (899), Expect = e-101
 Identities = 181/281 (64%), Positives = 214/281 (76%), Gaps = 2/281 (0%)

Query: 16  LISTPVFAAE--LTGTLKKIKESGTITLGHRDASIPFSYIADASGKPVGYSHDIQLKIVE 73
           L+ T V AAE  LTGTL KI  + +ITLG+RDAS+PFSY+ D SG+P+GYS D+  KIVE
Sbjct: 14  LLGTQVQAAEAPLTGTLSKIASANSITLGYRDASVPFSYVGDQSGQPMGYSVDLANKIVE 73

Query: 74  AIKKDLDMPNLQVKYNLVTSQTRIPLVQNGTVDVECGSTTNNVERQQQVDFSVGIFEIGT 133
            I++ L +P L+VKYNLVTSQTRIPLVQNGTVD+ECGST   VERQ+QV FS G   +  
Sbjct: 74  RIQQKLALPQLKVKYNLVTSQTRIPLVQNGTVDLECGSTGVTVERQKQVAFSYGFIYVKG 133

Query: 134 KLLSKKDSAYKDFADLKGKNVVTTAGTTSERILKSMNADKQMGMNVISAKDHGESFQMLE 193
           +LL+  DS  K FADL+GK+VVTTAGTT+ER LKS NAD ++ M VISAKDHGE+FQML+
Sbjct: 134 QLLTASDSGIKSFADLRGKSVVTTAGTTNERFLKSYNADHKIDMFVISAKDHGEAFQMLQ 193

Query: 194 TGRAVAFMMDDALLAGEMAKAKKPTDWAVTGTAQSNEIYGCMVRKGDAPFKKAVDDAIIA 253
           +GRA AF MDDALL GE AKA+ P  W V G  QS EIY CMVRK D  F   V+ A+  
Sbjct: 194 SGRAAAFYMDDALLYGERAKARDPHKWVVVGEEQSREIYSCMVRKDDPQFLALVNGALAD 253

Query: 254 TYKSGEINKIYEKWFMQPIPPKGLNLMFPMSEELKALIANP 294
            Y SGEIN IY++WF QPIPPKGLNL FPM+ ELKA+IA P
Sbjct: 254 LYSSGEINGIYQRWFEQPIPPKGLNLEFPMTSELKAIIAKP 294


Lambda     K      H
   0.315    0.131    0.365 

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: 3
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: 304
Length of database: 300
Length adjustment: 27
Effective length of query: 277
Effective length of database: 273
Effective search space:    75621
Effective search space used:    75621
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 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