Alignments for a candidate for TM0028 in Dechlorosoma suillum PS

GapMind for catabolism of small carbon sources

Alignments for a candidate for TM0028 in Dechlorosoma suillum PS

Align TM0028, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized)
to candidate Dsui_2799 Dsui_2799 oligopeptide/dipeptide ABC transporter, ATP-binding protein

Query= TCDB::Q9WXN5
         (330 letters)



>FitnessBrowser__PS:Dsui_2799
          Length = 670

 Score =  190 bits (483), Expect = 8e-53
 Identities = 122/323 (37%), Positives = 183/323 (56%), Gaps = 15/323 (4%)

Query: 5   LLKAENVRAYYKLEKVSVKAVDGLSFEILEDEVIGVVGESGCGKTTLSNVIFMNMVKPLT 64
           LL   N++A +      + AVDG+SF +   E   ++GESGCGK+  +  +   +     
Sbjct: 4   LLSVRNLKAGFLAGGRVLTAVDGVSFAVAPGETFALLGESGCGKSATALALLRLLPNAGR 63

Query: 65  LVDGKIFLRVNGEFVELSSMTRDEVKRKFWGKEITIIPQAAMNALMPTIRMEKYVRHLAE 124
           +  G+++L   GE  E+ ++  +   R   G    +I Q    +L P + + + +    E
Sbjct: 64  IQGGEVWLE--GE--EILALP-EAAMRDRRGSAAAMIFQEPATSLNPVLTIGRQIGESLE 118

Query: 125 SH-GIDEEELLDKARRRFEEVGL-DP-LWIKRYPFELSGGMRQRAVIAIATILNPSLLIA 181
            H G+  E    +A      VG+ DP   ++ YPF+LSGGM+QRA+IAIA    P LLIA
Sbjct: 119 RHRGMKGEAARREALALLTAVGIADPERRLEEYPFQLSGGMKQRAMIAIALAGEPRLLIA 178

Query: 182 DEPTSALDVVNQKVLLKVLMQMKRQGIVKSIIFITHDIATVRQIADRMIIMYAGKIVEFA 241
           DEPT+ALDV  Q  +L +L +++ +  +  ++ ITHD+  V + A R+ +MYAG+IVE A
Sbjct: 179 DEPTTALDVTIQAQILDLLARLQAERAM-GMLLITHDLGVVARSAHRVGVMYAGEIVETA 237

Query: 242 PVESLLEKPLHPYTQGLFNSVLTPEPEVKKRG--ITTIPGAPPNLINPPSGCRFHPRCPH 299
           P +     P HPYTQ LF ++    P++ +RG  + TIPG  P L   P+GCRF PRCP 
Sbjct: 238 PRQEFFASPRHPYTQKLFAAL----PDLGQRGAQLATIPGQVPGLAAMPAGCRFAPRCPV 293

Query: 300 AMDVCKEKEPPLTEIEPGRRVAC 322
           AMD C+ + P  TE+E G +V C
Sbjct: 294 AMDRCRLESPGWTELEAGHQVRC 316



 Score =  174 bits (442), Expect = 4e-48
 Identities = 114/334 (34%), Positives = 173/334 (51%), Gaps = 24/334 (7%)

Query: 2   KEILLKAENVRAYYKLEKV-------SVKAVDGLSFEILEDEVIGVVGESGCGKTTLSNV 54
           +E LL    ++ ++ + K         VKAVDG+S E+     + +VGESGCGKTT    
Sbjct: 348 RENLLAVGELKVHFPIRKGLFKRTVGHVKAVDGVSLELQRGRTLALVGESGCGKTTAGKA 407

Query: 55  IFMNMVKPLTLVDGKIFLRVNGEFVELSSMTRDEVKRKFWGKEITIIPQAAMNALMPTIR 114
           +       L L+     +R++G   EL  +   E+K     + + ++ Q    +L P + 
Sbjct: 408 V-------LRLLPATGSVRLDGR--ELLGLPERELKPL--RRRMQMVFQDPFASLNPRLT 456

Query: 115 MEKYVRH--LAESHGIDEEELLDKARRRFEEVGLDPLWIKRYPFELSGGMRQRAVIAIAT 172
           + + +     A       +E         E VGL    + RYP E SGG RQR  IA A 
Sbjct: 457 VGEIIEEGMTALRVAASRDERRAALAALLESVGLPAEALGRYPHEFSGGQRQRIAIARAL 516

Query: 173 ILNPSLLIADEPTSALDVVNQKVLLKVLMQMKRQGIVKSIIFITHDIATVRQIADRMIIM 232
            + P LL+ DEPTSALDV  Q  +L +L +++ + +  + +FITH+ A V  +A  + +M
Sbjct: 517 AVQPELLVCDEPTSALDVSVQAQILNLLRRLQEE-LGLAYLFITHNFAVVEYLAHDVAVM 575

Query: 233 YAGKIVEFAPVESLLEKPLHPYTQGLFNSVLTPEPEVK-KRGITTIPGAPPNLINPPSGC 291
           Y G+IVE  PV+ +L  P HPYT+ L ++V  PEP +  +R +  +PG  P+   PP GC
Sbjct: 576 YLGRIVEQGPVQQVLAAPCHPYTRALLSAV--PEPRLAGQREMVRLPGETPSPARPPQGC 633

Query: 292 RFHPRCPHAMDVCKEKEPPLTEIEPGRRVACWLY 325
            FHPRC  A + C+++ P  +    G  V C LY
Sbjct: 634 HFHPRCAQASERCRQEYPAPSTQAGGVVVRCHLY 667


Lambda     K      H
   0.321    0.138    0.405 

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: 561
Number of extensions: 26
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 330
Length of database: 670
Length adjustment: 33
Effective length of query: 297
Effective length of database: 637
Effective search space:   189189
Effective search space used:   189189
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: 51 (24.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources