GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gltI in Herbaspirillum seropedicae SmR1

Align Probable binding protein component of ABC transporter, component of Amino acid transporter, AatJMQP. Probably transports L-glutamic acid, D-glutamine acid, L-glutamine and N-acetyl L-glutamic acid (Johnson et al. 2008). Very similar to 3.A.1.3.19 of P. putida (characterized)
to candidate HSERO_RS19255 HSERO_RS19255 ABC transporter

Query= TCDB::Q9I402
         (302 letters)



>FitnessBrowser__HerbieS:HSERO_RS19255
          Length = 315

 Score =  292 bits (748), Expect = 6e-84
 Identities = 150/290 (51%), Positives = 199/290 (68%), Gaps = 1/290 (0%)

Query: 7   LLSTAIVAALLSAPVVADELTGTLKKIKETGTITLGHRDASIPFSYLGTEPGKPIGYSHD 66
           L    + A++L + V A+E TG LKKIK++GT+TLG RD+SIPFSYL  +     GYS D
Sbjct: 6   LAGVLVGASVLMSSVHAEEFTGRLKKIKDSGTLTLGVRDSSIPFSYLDDKQSYQ-GYSID 64

Query: 67  LQLKVVEAVKKELNLPELKVRYNLVTSQTRIPLVQNGTVDIECGSTTNNEERQKQVDFSV 126
           L LK   A++K+L L  L ++   VTS TRIPL+ NGT DI C S TNN+ER  QV FSV
Sbjct: 65  LCLKAATAIQKKLGLTSLNIKMVPVTSATRIPLIANGTTDISCDSATNNQERWNQVAFSV 124

Query: 127 GIFEVGTRLLSKKTANIKDFDDLKGKNVVTTAGTTSERLLKAMNADKKMGMNIISAKDHG 186
             F    + LSKK AN+K  +DLKGK VV+T+GT++ + + A+NA++ +GMNI++AKDH 
Sbjct: 125 TEFVTANKFLSKKAANLKTLEDLKGKTVVSTSGTSNLKQITALNAERNLGMNILAAKDHA 184

Query: 187 ESFMMLESGRAVAFMMDDALLYGEMAKAKKPDDWVVGGTPQSFEIYGCMVRKGDAAFKKV 246
           E+F+M+E+GRA AF+MDD LL    A +K P D+ V     S E YG ++ KGD  FK V
Sbjct: 185 EAFLMVETGRAAAFVMDDILLSSLAANSKAPGDYQVSSEALSVEPYGLILPKGDKEFKTV 244

Query: 247 VDKAITDTYASGEVNKIYDKWFTQPIPPKGLNLNFPMSEELKKLIASPTD 296
           VD A+T  Y   ++ KIY KWF  PIPPKG+NLN PMS +L+ ++A PTD
Sbjct: 245 VDDALTVVYKGDDIKKIYAKWFQSPIPPKGVNLNVPMSPQLQAVLAKPTD 294


Lambda     K      H
   0.314    0.132    0.370 

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: 275
Number of extensions: 7
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: 302
Length of database: 315
Length adjustment: 27
Effective length of query: 275
Effective length of database: 288
Effective search space:    79200
Effective search space used:    79200
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: 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