GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SM_b21216 in Marinobacter adhaerens HP15

Align ABC transporter for D-Glucosamine, ATPase component (characterized)
to candidate GFF3011 HP15_2955 ATP-binding component of ABC transporter

Query= reanno::Smeli:SM_b21216
         (360 letters)



>FitnessBrowser__Marino:GFF3011
          Length = 372

 Score =  341 bits (875), Expect = 2e-98
 Identities = 190/371 (51%), Positives = 249/371 (67%), Gaps = 16/371 (4%)

Query: 1   MSALEIRNIRKRYGEV--ETLKGIDIALESGEFLVLLGSSGCGKSTLLNIIAGLAEPSGG 58
           MS LE+R+IRK Y  V  ETLKGIDI + SGEFL+L+G SGCGKSTL+N IAGL   + G
Sbjct: 1   MSQLELRSIRKTYPGVAEETLKGIDIDIASGEFLILVGPSGCGKSTLMNTIAGLETITDG 60

Query: 59  DILIGERSVLGVHPKDRDIAMVFQSYALYPNLSVARNIGFGLEMRRVPQAEHDKAVRDTA 118
            I++  + +  + PKDRDIAMVFQSYALYP +SV  NI FGL++R +P+ E D+ V   A
Sbjct: 61  SIVLDGKDISTMEPKDRDIAMVFQSYALYPTMSVRENIAFGLKIRGLPKHEIDQEVERVA 120

Query: 119 RLLQIENLLDRKPSQLSGGQRQRVAIGRALVRNPQVFLFDEPLSNLDAKLRMEMRTELKR 178
            LLQI  L+++KP+ LSGGQ+QRVA+GRAL R P+++LFDEPLSNLDAKLR+EMRTE+K+
Sbjct: 121 DLLQISPLMNKKPANLSGGQQQRVAMGRALARRPRIYLFDEPLSNLDAKLRVEMRTEIKK 180

Query: 179 LHQMLRTTVVYVTHDQIEAMTLATRIAVMRDGRIEQLAAPDEVYDRPATLYVAGFVGSPP 238
           LHQ L+TT+VYVTHDQIEAMTLA RIAV++DG ++QL  P EVYDRP  L+VAGF+GSP 
Sbjct: 181 LHQRLKTTIVYVTHDQIEAMTLADRIAVLKDGELQQLGTPKEVYDRPENLFVAGFMGSPA 240

Query: 239 MNI--LDAEMTANGLKIE-----GCEEVLPLPAAFNGAAWAGRRVKVGIRPEALRLAAGS 291
           M+   +  E    GL+ E     G    LP+P     A   G++V +GIRPE +      
Sbjct: 241 MSFVPVTVEQGEGGLQAEVRGNDGRSVKLPVPEFL--ADRVGKKVILGIRPEHITQPQDQ 298

Query: 292 E-AQRLTA----SVEVVELTGPELVTTATVGSQRITACLPPRTAVGMGSAHAFTFDGTAL 346
           +  Q L A    ++EV E TGP+++    +    +   + P   V  G      FD   +
Sbjct: 299 KNDQTLVAKGEFTIEVTEPTGPDVIALIQLNDTNVHCRIDPEHPVTWGETAELMFDMKKV 358

Query: 347 HLFDPESGRSL 357
             FDPE+ + +
Sbjct: 359 VFFDPETEKRI 369


Lambda     K      H
   0.320    0.136    0.385 

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: 379
Number of extensions: 13
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: 360
Length of database: 372
Length adjustment: 30
Effective length of query: 330
Effective length of database: 342
Effective search space:   112860
Effective search space used:   112860
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