GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc02869 in Herbaspirillum seropedicae SmR1

Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate HSERO_RS22750 HSERO_RS22750 sugar ABC transporter ATP-binding protein

Query= reanno::Smeli:SMc02869
         (352 letters)



>FitnessBrowser__HerbieS:HSERO_RS22750
          Length = 377

 Score =  330 bits (845), Expect = 5e-95
 Identities = 180/358 (50%), Positives = 232/358 (64%), Gaps = 28/358 (7%)

Query: 20  LQLKTIRKAF-GSHEVLKGIDLDVKDGEFVIFVGPSGCGKSTLLRTIAGLEDATSGSVQI 78
           + +K +RK + G  +VL G++LD++DGEF + VGPSGCGKSTLLR + GLE+ + G + I
Sbjct: 4   VNIKQLRKTYDGRADVLAGLNLDIRDGEFCVLVGPSGCGKSTLLRMLCGLEEISGGELAI 63

Query: 79  DGVEVGHVAPAKRGIAMVFQSYALYPHLTVKDNMGLGLKQAGVPKAEIEEKVAKAAGMLS 138
            G  V H+ PA+RGIAMVFQSYALYPH+ V  NM  GLK AG  K++I+ ++  AA +L 
Sbjct: 64  GGQVVNHLPPAERGIAMVFQSYALYPHMNVYKNMAFGLKVAGNSKSDIDARIRHAAAILK 123

Query: 139 LEPYLARRPAELSGGQRQRVAIGRAIVREPKLFLFDEPLSNLDAALRVNTRLEIARLHRS 198
           ++  L R P ELSGGQRQRVAIGRAIVR+P+LFLFDEPLSNLDAALRV TRLEIA+LHR 
Sbjct: 124 IDHLLQRLPRELSGGQRQRVAIGRAIVRQPRLFLFDEPLSNLDAALRVQTRLEIAKLHRQ 183

Query: 199 LKATMIYVTHDQVEAMTLADKIVVLNAGRIEQVGSPMELYNRPANLFVAGFIGSPQMNF- 257
           L AT++YVTHDQVEAMTL DKIVV++ GRI+Q G+P+ELY +P NLFVAGFIGSP+MNF 
Sbjct: 184 LAATIVYVTHDQVEAMTLGDKIVVMHEGRIQQAGTPLELYQQPQNLFVAGFIGSPKMNFF 243

Query: 258 -------------------------IEAAKLGDGEAKTIGIRPEHIGLSRESGD-WKGKV 291
                                    ++   +  G A T+G+R E I      G    G V
Sbjct: 244 QGVVTRCDDSGVQVEIAGGLRLLADVDPLGVTPGAAVTLGLRAEQIREGLGDGQPLHGVV 303

Query: 292 IHVEHLGADTIIYIESETVGLLTVRLFGEHRYATDDIVHATPVIGSMHRFDADGRVIK 349
             VEHLG    +Y+  +    + VR  G         +  +    + H FDA G+ ++
Sbjct: 304 NLVEHLGEANFLYVTLDGGHDIVVRGDGNRNVDIGQPIALSVHSHAFHLFDAQGQALR 361


Lambda     K      H
   0.320    0.137    0.393 

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: 401
Number of extensions: 12
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: 352
Length of database: 377
Length adjustment: 29
Effective length of query: 323
Effective length of database: 348
Effective search space:   112404
Effective search space used:   112404
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 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