GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lacK in Alicycliphilus denitrificans K601

Align ABC transporter for Lactose, ATPase component (characterized)
to candidate WP_013723230.1 ALIDE2_RS22605 putative 2-aminoethylphosphonate ABC transporter ATP-binding protein

Query= reanno::Smeli:SM_b20002
         (358 letters)



>NCBI__GCF_000204645.1:WP_013723230.1
          Length = 377

 Score =  227 bits (578), Expect = 4e-64
 Identities = 126/313 (40%), Positives = 196/313 (62%), Gaps = 20/313 (6%)

Query: 4   LQLSDVRKSYGGLEVIKGVDLDIKSGEFVVFVGPSGCGKSTLLRMIAGLEEISSGDLTID 63
           L++  + K++     ++ +DL ++ GE + F+GPSGCGK+TLLR+IAGLE  +SG +   
Sbjct: 20  LEIKGIHKNFENFSALRDIDLTVRQGEMLCFLGPSGCGKTTLLRIIAGLETQTSGSIVQS 79

Query: 64  DVRMNDVDPSKRGIAMVFQSYALYPHMTVRENMGFALRFAGVPRAEIEKRVNEAAHILEL 123
              ++ +  S+R   +VFQSYAL+P++T+ EN+ + L    + +AEI+ RV E   +  L
Sbjct: 80  GRDISWLPASERDYGIVFQSYALFPNLTIAENVAYGLVNGKMRKAEIQARVAELLAMAGL 139

Query: 124 GALLDRKPKQLSGGQRQRVAIGRAIVRHPKIFLFDEPLSNLDAELRVHMRIEIARLHKQL 183
                + P QLSGGQ+QRVA+ RA+  +P + L DEPLS LDA +RV +R EI RL KQ+
Sbjct: 140 PTAGGKYPSQLSGGQQQRVALARALATNPGLLLLDEPLSALDATVRVRLRAEIRRLQKQV 199

Query: 184 ATTIVYVTHDQVEAMTLADKIVVMRAGVVEQVGSPLDLYDDPANLFVAGFIGSPKMNFLK 243
             T + VTHDQ EA++++D+IVVM  GV+EQVG+P+++Y+ PA+ FVA F+G  K+N L+
Sbjct: 200 GITTIMVTHDQEEALSMSDRIVVMNHGVIEQVGTPMEIYERPASPFVANFVG--KVNVLR 257

Query: 244 GVIEIDEDQAYARLPDYGDAKIPVTLQAAAGT-----AVTIGIRP-----EHFDEAGPAA 293
           G       QA      +   K+ +  +A+ G+      V++ +RP     EH +   P  
Sbjct: 258 G-------QALGG-KRFRVGKMEIECEASEGSFRLGEDVSLYLRPEDRVAEHLEAGTPYR 309

Query: 294 LDLAIDMLEHLGG 306
           L + ++ +E LGG
Sbjct: 310 LGVLVNKVEFLGG 322


Lambda     K      H
   0.321    0.139    0.396 

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: 353
Number of extensions: 18
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: 358
Length of database: 377
Length adjustment: 30
Effective length of query: 328
Effective length of database: 347
Effective search space:   113816
Effective search space used:   113816
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Apr 09 2024. 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