GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lacK in Halomonas xinjiangensis TRM 0175

Align ABC transporter for Lactose, ATPase component (characterized)
to candidate WP_043527041.1 JH15_RS03500 sn-glycerol-3-phosphate import ATP-binding protein UgpC

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



>NCBI__GCF_000759345.1:WP_043527041.1
          Length = 354

 Score =  320 bits (819), Expect = 5e-92
 Identities = 178/361 (49%), Positives = 243/361 (67%), Gaps = 19/361 (5%)

Query: 1   MSELQLSDVRKSYGG-LEVIKGVDLDIKSGEFVVFVGPSGCGKSTLLRMIAGLEEISSGD 59
           M+ +QL+ ++K+Y G +E +KG+DL+I  GEFVV VGPSGCGKSTLLRM+AGLE I+ G 
Sbjct: 1   MASIQLTGLKKTYAGNVEAVKGIDLEIADGEFVVLVGPSGCGKSTLLRMVAGLETITDGT 60

Query: 60  LTIDDVRMNDVDPSKRGIAMVFQSYALYPHMTVRENMGFALRFAGVPRAEIEKRVNEAAH 119
           L IDD  +ND++P++R IAMVFQ+YALYPHMTV  N+ + L+  GV R EIE+RV++AA 
Sbjct: 61  LKIDDRVVNDLEPAERDIAMVFQNYALYPHMTVFGNLAYGLKNRGVKREEIERRVHDAAA 120

Query: 120 ILELGALLDRKPKQLSGGQRQRVAIGRAIVRHPKIFLFDEPLSNLDAELRVHMRIEIARL 179
           +LE+   L+RKP++LSGGQRQRVA+GRA+VR P  FLFDEPLSNLDA+LRV MR+EI +L
Sbjct: 121 MLEIEPFLERKPRKLSGGQRQRVAMGRALVREPSAFLFDEPLSNLDAKLRVQMRVEIKQL 180

Query: 180 HKQLATTIVYVTHDQVEAMTLADKIVVMRAGVVEQVGSPLDLYDDPANLFVAGFIGSPKM 239
            ++L TT +YVTHDQ+EA+TL D++VV+  G +EQVG+P+++Y+ PA++FVA FIGSP M
Sbjct: 181 QRRLKTTSLYVTHDQLEALTLGDRLVVLNGGSIEQVGTPMEVYEKPASMFVATFIGSPAM 240

Query: 240 NFLKGVIEIDEDQAYARLPDYGDAKIPVTLQAAAGTAVTIGIRPEHFDEAGPAALDL--- 296
           N L  V  + E  A   L              AA T V IGIRP+      P    L   
Sbjct: 241 NMLP-VAYLRERGANGLLD-----------HLAADTDV-IGIRPDDLRIEAPDEDHLVVT 287

Query: 297 -AIDMLEHLGGETFAYARHHGNGELIVVETKNGRGLKTGDRLTARFDPVSVLVFD-GEGK 354
             +++ E  G E+  Y    G+ +  V+ T     +  G+ +     P ++  F+   GK
Sbjct: 288 GTVELFEAAGAESHLYVSLEGSDQPTVIRTSARPPVAEGETMRFHVLPSALHPFNQASGK 347

Query: 355 R 355
           R
Sbjct: 348 R 348


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: 372
Number of extensions: 10
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: 358
Length of database: 354
Length adjustment: 29
Effective length of query: 329
Effective length of database: 325
Effective search space:   106925
Effective search space used:   106925
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 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