GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livJ in Pantoea rwandensis LMG 26275

Align leucine-specific-binding protein LivK (characterized)
to candidate WP_084936137.1 HA51_RS18910 branched-chain amino acid ABC transporter substrate-binding protein

Query= CharProtDB::CH_107418
         (369 letters)



>NCBI__GCF_002095475.1:WP_084936137.1
          Length = 375

 Score =  553 bits (1424), Expect = e-162
 Identities = 266/369 (72%), Positives = 314/369 (85%), Gaps = 5/369 (1%)

Query: 6   KTIIAGMIALAISHTAMADDIKVAVVGAMSGPIAQWGDMEFNGARQAIKDINAKGGIKGD 65
           + ++AG +ALA+SH A+A DIK+A+VGA +GP+AQ+GDM+F GA QAIKDINAKGG+ GD
Sbjct: 7   RALLAGCVALALSHAALAKDIKIAIVGAATGPVAQYGDMQFTGAAQAIKDINAKGGVNGD 66

Query: 66  KLVGVEYDDACDPKQAVAVANKIVNDGIKYVIGHLCSSSTQPASDIYEDEGILMISPGAT 125
           KLVGVEYDDACDPKQAVAVANK+VNDGIKYVIGHLCSSSTQPASDIY DEGILMI+P AT
Sbjct: 67  KLVGVEYDDACDPKQAVAVANKVVNDGIKYVIGHLCSSSTQPASDIYNDEGILMITPAAT 126

Query: 126 NPELTQRGYQHIMRTAGLDSSQGPTAAKYILETVKPQRIAIIHDKQQYGEGLARSVQDGL 185
            PELT RGY  ++RT GLDS QGPTAA YIL  +KP+RIA++HDKQQYG+GLA SVQ  L
Sbjct: 127 APELTARGYADVLRTTGLDSDQGPTAATYILNEIKPKRIAVVHDKQQYGQGLAESVQKTL 186

Query: 186 KAANANVVFFDGITAGEKDFSALIARLKKENIDFVYYGGYYPEMGQMLRQARSVGLKTQF 245
           KA   NVV F+GITAG+KDFS LIARLKKEN+DFVYYGGYYPE+GQ+LRQA++ GL   F
Sbjct: 187 KAKGGNVVLFEGITAGDKDFSTLIARLKKENVDFVYYGGYYPELGQILRQAKAAGLNAGF 246

Query: 246 MGPEGVGNASLSNIAGDAAEGMLVTMPKRYDQDPANQGIVDALKA----DKKDPSGPYVW 301
           MGPEGVGNASLSNIAGDA+EG+ VT+PKRYDQ P N+ IV+A+KA    ++KDP+GP+VW
Sbjct: 247 MGPEGVGNASLSNIAGDASEGLYVTLPKRYDQLPENKAIVEAIKANTASNRKDPTGPFVW 306

Query: 302 ITYAAVQSLATALERTGSDEPLALVKDLKANGA-NTVIGPLNWDEKGDLKGFDFGVFQWH 360
            TYAA+QSL   +ER+ S EP A+ K+LK   A  TV+G LNWD+KGDLKGF+FGVF+WH
Sbjct: 307 TTYAAIQSLVAGIERSKSAEPDAIAKNLKEGAAVPTVMGNLNWDQKGDLKGFEFGVFKWH 366

Query: 361 ADGSSTAAK 369
            DGSSTA K
Sbjct: 367 KDGSSTAVK 375


Lambda     K      H
   0.315    0.133    0.386 

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: 570
Number of extensions: 15
Number of successful extensions: 3
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: 369
Length of database: 375
Length adjustment: 30
Effective length of query: 339
Effective length of database: 345
Effective search space:   116955
Effective search space used:   116955
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 (21.5 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 24 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