GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsD in Collinsella tanakaei YIT 12063

Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate WP_009140593.1 HMPREF9452_RS02825 ATP-binding cassette domain-containing protein

Query= reanno::pseudo13_GW456_L13:PfGW456L13_1897
         (386 letters)



>NCBI__GCF_000225705.1:WP_009140593.1
          Length = 356

 Score =  155 bits (392), Expect = 2e-42
 Identities = 116/364 (31%), Positives = 177/364 (48%), Gaps = 31/364 (8%)

Query: 8   NVNKTYGPGLPDTLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGGAILV--- 64
           ++ K Y    PD   ++ L+   GE + L+G SGCGKS  + CIAG+ET   G I V   
Sbjct: 6   DIKKAY----PDFSLDVRLEAA-GERVALLGASGCGKSCTLRCIAGVETPDEGRIAVNGV 60

Query: 65  ---DDADISGMSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEVARVSK 121
              D A    +SP+ R  A++FQ+Y L+P +SV DN+  G++ R       DE   R   
Sbjct: 61  TFFDSARGINLSPQQRKCALLFQNYQLFPNLSVADNVLAGVEGRLSREGR-DELARRYLS 119

Query: 122 LLQIEHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKLM 181
           +  +     R P +LSGGQQQRVA+ R LA RP IY+FDEP S LD+ L+  +   +  +
Sbjct: 120 IFGMAGYADRYPARLSGGQQQRVALARMLAARPAIYMFDEPFSALDSFLKSALEQNLLDL 179

Query: 182 HQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFIGSPPM 241
              + +T +YV+HD  EA  L +++ V+ +G +++ GT + +   P  L      G    
Sbjct: 180 FSVIDSTVLYVSHDIDEACRLCERICVLHNGRVEEDGTVEQVVQRPQTLAALRLTGCKNT 239

Query: 242 NFIPLRLQRKDGRLLALLDSGQARCELPLGMQDAGLEDREVILGIRPEQIILANGEANGL 301
           +    R ++    L+  LD G       +G   A + D    LG+R     + N EA G 
Sbjct: 240 S----RARKVGDTLVEALDWGMT---FDVG---APVADDVAYLGVRANYFHIDNREAPGK 289

Query: 302 PTIRAEVQVTEPTGPDTLVFVNLNDTKVCCRL-------APDVA--PAVGETLTLQFDPA 352
            +    V     +  + LV ++        RL         D+A  P  G+ L + FD A
Sbjct: 290 NSYMLRVARVSDSRFERLVLLDPPRADASSRLTWKVNTVGADMATLPREGDCLRMHFDAA 349

Query: 353 KVLL 356
           K+L+
Sbjct: 350 KILM 353


Lambda     K      H
   0.319    0.138    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: 343
Number of extensions: 15
Number of successful extensions: 4
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: 386
Length of database: 356
Length adjustment: 30
Effective length of query: 356
Effective length of database: 326
Effective search space:   116056
Effective search space used:   116056
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 (21.7 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