GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_2396 in Herbaspirillum aquaticum IEH 4430

Align Branched chain amino acid ABC transporter substrate-binding protein (characterized, see rationale)
to candidate WP_088755389.1 CEJ45_RS12295 branched-chain amino acid ABC transporter substrate-binding protein

Query= uniprot:A0A165KTD4
         (375 letters)



>NCBI__GCF_002213425.1:WP_088755389.1
          Length = 381

 Score =  419 bits (1076), Expect = e-122
 Identities = 218/377 (57%), Positives = 270/377 (71%), Gaps = 7/377 (1%)

Query: 4   KLKLTVVA-AIAAA---AGVASAQEQVVKIGHVAPVSGAQAHYGKDNENGARMAIEELNA 59
           K+K+  VA A+ AA   AG A AQE V+KIGHVAP++G  AH GKDNENGARMA++ELNA
Sbjct: 3   KIKMIPVATALVAAFSFAGAAQAQE-VIKIGHVAPLTGPNAHIGKDNENGARMAVDELNA 61

Query: 60  QGVTIGGKKIKFELVAEDDAADPKQGTAAAQKLCDAKVAGVVGHLNSGTTIPASKVYNDC 119
           +G  IGGKK+ F+LV +DDA+DPKQ T  AQ L DAKV GVVGH+NSGTTIPASK+Y D 
Sbjct: 62  KGFEIGGKKVTFQLVPQDDASDPKQATTVAQALVDAKVKGVVGHMNSGTTIPASKIYYDA 121

Query: 120 GIPHVTGAATNPNLTKPGYKTTFRIIANDNALGAGLAFYAVDTLKLKTVAIIDDRTAYGQ 179
           GIP ++ +ATNP  T+ G+ T FR++AND  LG  L  YAV+ LK K VA+IDDRTAYGQ
Sbjct: 122 GIPQISPSATNPKYTQQGFNTAFRVVANDGQLGGVLGRYAVNELKGKNVAVIDDRTAYGQ 181

Query: 180 GVADVFKKTATAKGMKVVDEQFTTDKATDFMAILTAIKAKNPDAIFYGGMDPQGGPMLRQ 239
           GVA+ F+K+A A G  +V  Q+TTDKATDF AILT++K+K PD +F+GGMD   GPMLRQ
Sbjct: 182 GVAEEFRKSALAAGATIVATQYTTDKATDFNAILTSVKSKKPDLVFFGGMDAVAGPMLRQ 241

Query: 240 MEQLGMGNVKYFGGDGICTSEIAKLAAGAKTLGNVICAE-GGSSLAKMPGGTAWKAKYDA 298
           M+QLG+   K+ GGDGICT+E+  LA        V+CAE GG + A       +KA Y  
Sbjct: 242 MDQLGVA-AKFMGGDGICTTELPSLAGAGLKDSEVVCAEAGGVTEAGKKPLEDFKAAYKK 300

Query: 299 KYPNQFQVYSPYTYDATFLIVDAMKRANSVDPKVYTPELAKSSFKGVTSTIAFEPNGEMK 358
           K+     +Y+PYTYDA   + DAMK+A S DPKVY P LAK   KGVT  IAF+  G++ 
Sbjct: 301 KFNQDVVIYAPYTYDALMTLADAMKQAGSSDPKVYLPVLAKIKHKGVTGEIAFDAKGDIL 360

Query: 359 NPAITLYVYKDGKKTPL 375
           N  +TLY YK GK+T L
Sbjct: 361 NGTLTLYTYKGGKRTLL 377


Lambda     K      H
   0.315    0.131    0.375 

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: 522
Number of extensions: 20
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: 375
Length of database: 381
Length adjustment: 30
Effective length of query: 345
Effective length of database: 351
Effective search space:   121095
Effective search space used:   121095
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: 50 (23.9 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