GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hisJ in Methylobacterium nodulans ORS 2060

Align histidine ABC transporter, periplasmic histidine-binding protein HisJ (characterized)
to candidate WP_015933040.1 MNOD_RS31675 transporter substrate-binding domain-containing protein

Query= CharProtDB::CH_018185
         (260 letters)



>NCBI__GCF_000022085.1:WP_015933040.1
          Length = 256

 Score =  126 bits (317), Expect = 4e-34
 Identities = 83/257 (32%), Positives = 131/257 (50%), Gaps = 4/257 (1%)

Query: 1   MKKLALSLSLVLAFSSATAAFAAIPQKIRIGTDPTYAPFESKNAQGELVGFDIDLAKELC 60
           M +L   L ++++ +++    A +P  +RI T+    PF      G+  GF++DLA+ LC
Sbjct: 1   MSRLLSRLLVLVSLAASPVQAAPLPDPVRIATEGGNPPFNYVE-DGKPAGFEVDLAEALC 59

Query: 61  KRINTQCTFVENPLDALIPSLKAKKIDAIMSSLSITEKRQQEIAFTDKLYAADSRLVVAK 120
           K     C  V +  D +I  L+  + DAIM+SL+IT KR+  I+F+   Y   S  +  +
Sbjct: 60  KAAGLTCRIVLHQWDGIIRGLEGAEYDAIMASLAITPKRRSRISFSRSYYRIPSSYMARR 119

Query: 121 NSDIQP-TVASLKGKRVGVLQGTTQETFGNEHWAPKGIEIVSYQGQDNIYSDLTAGRIDA 179
           +    P   A+LKG+ VG    + Q  +  E  AP+  +I S+    +   DL  GR+D 
Sbjct: 120 DDQTGPLDPAALKGRAVGAAAHSPQLAY-LEARAPEA-DIRSFDSVKDAGYDLRLGRLDL 177

Query: 180 AFQDEVAASEGFLKQPVGKDYKFGGPAVKDEKLFGVGTGMGLRKEDNELREALNKAFAEM 239
              D+   +E           +  G     + L G G G+GLRK D+ LREA ++A A +
Sbjct: 178 VLGDKRELTEILALPDGAACCRLVGDVPPGDPLLGEGVGIGLRKGDDALREAFDRAIAAV 237

Query: 240 RADGTYEKLAKKYFDFD 256
            ADGTY+++  KY  FD
Sbjct: 238 IADGTYDRIRAKYLPFD 254


Lambda     K      H
   0.316    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: 144
Number of extensions: 7
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: 260
Length of database: 256
Length adjustment: 24
Effective length of query: 236
Effective length of database: 232
Effective search space:    54752
Effective search space used:    54752
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 Apr 09 2024. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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