GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gltI in Acidovorax sp. GW101-3H11

Align ABC transporter for L-asparagine and L-glutamate, periplasmic substrate-binding component (characterized)
to candidate Ac3H11_1955 Glutamate Aspartate periplasmic binding protein precursor GltI (TC 3.A.1.3.4)

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



>FitnessBrowser__acidovorax_3H11:Ac3H11_1955
          Length = 299

 Score =  239 bits (611), Expect = 4e-68
 Identities = 128/296 (43%), Positives = 179/296 (60%), Gaps = 4/296 (1%)

Query: 6   HILGAAIAAALISTPVFAAELTGTLKKIKESGTITLGHRDASIPFSYIADASGKPVGYSH 65
           H+L  A+ A    +    A+ T TL KIK SG++TLG R++S   SY    +GK VG+  
Sbjct: 4   HLLAIAVTALAAGSAF--AQATDTLAKIKASGSVTLGVRESS-GLSYTL-GNGKYVGFHT 59

Query: 66  DIQLKIVEAIKKDLDMPNLQVKYNLVTSQTRIPLVQNGTVDVECGSTTNNVERQQQVDFS 125
           ++   ++  ++K L +P L +KY  VTSQ RIPLV NGTVD+ECGSTTNN  R + V F+
Sbjct: 60  EMGEIVLADVQKQLGLPKLDIKYQPVTSQNRIPLVTNGTVDLECGSTTNNAARLKDVSFA 119

Query: 126 VGIFEIGTKLLSKKDSAYKDFADLKGKNVVTTAGTTSERILKSMNADKQMGMNVISAKDH 185
           V  +    +++ K +S      DL GK V TT GTTS + L+       +    +  KDH
Sbjct: 120 VTTYVEEVRMVVKANSGITSIKDLNGKTVATTTGTTSVQTLRKHERAGGIDFKEVMGKDH 179

Query: 186 GESFQMLETGRAVAFMMDDALLAGEMAKAKKPTDWAVTGTAQSNEIYGCMVRKGDAPFKK 245
            +SF MLETGRA AF+MD ++LA  ++K+K P D+ + G   + E   CM+RK D  FKK
Sbjct: 180 ADSFLMLETGRAEAFVMDGSILAANISKSKSPADYKIVGEVLNVEPIACMLRKDDPAFKK 239

Query: 246 AVDDAIIATYKSGEINKIYEKWFMQPIPPKGLNLMFPMSEELKALIANPTDKAADE 301
           AVDD+I    K G + K+Y+KWFMQP+PP  + +  PMS+  K   ANP DK  ++
Sbjct: 240 AVDDSIKRQIKDGSLAKLYDKWFMQPVPPANVKIGLPMSDATKEAWANPNDKPMED 295


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: 253
Number of extensions: 12
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: 304
Length of database: 299
Length adjustment: 27
Effective length of query: 277
Effective length of database: 272
Effective search space:    75344
Effective search space used:    75344
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