GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hisJ in Escherichia coli BW25113

Align histidine ABC transporter, periplasmic histidine-binding protein HisJ (characterized)
to candidate 16417 b2310 lysine/arginine/ornithine transporter subunit (NCBI)

Query= CharProtDB::CH_014295
         (260 letters)



>FitnessBrowser__Keio:16417
          Length = 260

 Score =  366 bits (940), Expect = e-106
 Identities = 175/259 (67%), Positives = 217/259 (83%)

Query: 1   MKKLVLSLSLVLAFSSATAAFAAIPQNIRIGTDPTYAPFESKNSQGELVGFDIDLAKELC 60
           MKK +L+LSL++  S+A +++AA+P+ +RIGTD TYAPF SK+++G+ VGFDIDL  E+C
Sbjct: 1   MKKSILALSLLVGLSTAASSYAALPETVRIGTDTTYAPFSSKDAKGDFVGFDIDLGNEMC 60

Query: 61  KRINTQCTFVENPLDALIPSLKAKKIDAIMSSLSITEKRQQEIAFTDKLYAADSRLVVAK 120
           KR+  +CT+V +  DALIPSLKAKKIDAI+SSLSIT+KRQQEIAF+DKLYAADSRL+ AK
Sbjct: 61  KRMQVKCTWVASDFDALIPSLKAKKIDAIISSLSITDKRQQEIAFSDKLYAADSRLIAAK 120

Query: 121 NSDIQPTVESLKGKRVGVLQGTTQETFGNEHWAPKGIEIVSYQGQDNIYSDLTAGRIDAA 180
            S IQPT++SLKGK VGVLQG+TQE + NE W  KG+++V+Y  QD +YSDL AGR+DAA
Sbjct: 121 GSPIQPTLDSLKGKHVGVLQGSTQEAYANETWRSKGVDVVAYANQDLVYSDLAAGRLDAA 180

Query: 181 FQDEVAASEGFLKQPVGKDYKFGGPSVKDEKLFGVGTGMGLRKEDNELREALNKAFAEMR 240
            QDEVAASEGFLKQP GKD+ F G SVKD+K FG GTG+GLRK+D EL  A NKA  E+R
Sbjct: 181 LQDEVAASEGFLKQPAGKDFAFAGSSVKDKKYFGDGTGVGLRKDDAELTAAFNKALGELR 240

Query: 241 ADGTYEKLAKKYFDFDVYG 259
            DGTY+K+AKKYFDF+VYG
Sbjct: 241 QDGTYDKMAKKYFDFNVYG 259


Lambda     K      H
   0.315    0.133    0.372 

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: 266
Number of extensions: 7
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: 260
Length of database: 260
Length adjustment: 24
Effective length of query: 236
Effective length of database: 236
Effective search space:    55696
Effective search space used:    55696
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: 47 (22.7 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