Alignments for a candidate for TM0028 in Marinobacter adhaerens HP15

GapMind for catabolism of small carbon sources

Alignments for a candidate for TM0028 in Marinobacter adhaerens HP15

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 GFF2860 HP15_2804 oligopeptide/dipeptide ABC transporter, ATP-binding protein-like protein

Query= TCDB::Q9WXN5
         (330 letters)



>FitnessBrowser__Marino:GFF2860
          Length = 672

 Score =  183 bits (465), Expect = 9e-51
 Identities = 115/321 (35%), Positives = 177/321 (55%), Gaps = 9/321 (2%)

Query: 5   LLKAENVRAYYKLEKVSVKAVDGLSFEILEDEVIGVVGESGCGKTTLSNVIFMNMVKPLT 64
           +L  +++      +  ++ AV G+S E+   E +G+VGESG GK+ ++ +  MN++ P  
Sbjct: 6   ILDIQDLSVDIPTDSSTLHAVRGISLELNRGETLGIVGESGSGKS-MTALALMNLLPPAA 64

Query: 65  LVDGKIFLRVNGEFVELSSMTRDEVKRKFWGKEITIIPQAAMNALMPTIRMEKYVRHLAE 124
                    ++ +  +L+  T  E+  K  G+ I +I Q  M +L P   + + ++    
Sbjct: 65  KRQASC---IDFDGSDLTHATERELASKIRGQRIGMIFQEPMTSLNPVYSIGRQLKETMT 121

Query: 125 SHG-IDEEELLDKARRRFEEVGL-DPLW-IKRYPFELSGGMRQRAVIAIATILNPSLLIA 181
            H  + + E  ++A    E+VGL DP   +K+YP ELSGG RQR +IA+A +  P LLIA
Sbjct: 122 LHRKVSDTEAENRAVYLLEKVGLPDPASRLKQYPHELSGGQRQRVMIAMALMNEPELLIA 181

Query: 182 DEPTSALDVVNQKVLLKVLMQMKRQGIVKSIIFITHDIATVRQIADRMIIMYAGKIVEFA 241
           DEPT+ALDV  Q  +L +L ++ +Q    S+I ITHD+  V + AD + +MYAG IVE  
Sbjct: 182 DEPTTALDVTIQAQILHLLREL-QQEFGMSMILITHDLGVVSRAADNIAVMYAGDIVETG 240

Query: 242 PVESLLEKPLHPYTQGLFNSVLTPEPEVKKRGITTIPGAPPNLINPPSGCRFHPRCPHAM 301
               +LE P HPYT+GL   V   + + ++R +  IPG  P +    SGC F  RCP A 
Sbjct: 241 KTGEVLENPRHPYTKGLLECVPGYKGQSQQR-LGAIPGIVPAMTGDISGCAFASRCPRAA 299

Query: 302 DVCKEKEPPLTEIEPGRRVAC 322
            VC+   PP  ++  GR   C
Sbjct: 300 GVCRTTNPPTKKLHQGRYFVC 320



 Score =  178 bits (452), Expect = 3e-49
 Identities = 119/306 (38%), Positives = 170/306 (55%), Gaps = 23/306 (7%)

Query: 22  VKAVDGLSFEILEDEVIGVVGESGCGKTTLSNVIFMNMVKPLTLVDGKIFLRVNGEFVE- 80
           ++A+D +S  + + EV+ +VGESGCGKTTL+  I M +  P T   G + L  NG+ +E 
Sbjct: 375 LQALDDVSLTLKKGEVLALVGESGCGKTTLTRTI-MGLQAPST---GSVTL--NGQRIEN 428

Query: 81  LSSMTRDEVKRKFWGKEITIIPQAAMNALMPTIRMEKYVRHLAESHGI-DEEELLDKARR 139
           L  M R         + I  I Q   ++L P   + + +      HGI   +E   + R+
Sbjct: 429 LPPMDR--------ARMIQPIFQDPYSSLNPRKTIGEIIAKPLFVHGIGSNQEQHQQVRK 480

Query: 140 RFEEVGLDPLWIKRYPFELSGGMRQRAVIAIATILNPSLLIADEPTSALDVVNQKVLLKV 199
             E VGL       YP +LSGG RQRA I  A ILNP ++I DEPTSALDV  Q  +L +
Sbjct: 481 MMELVGLPSRVFNSYPDQLSGGQRQRAAIGRALILNPEVVICDEPTSALDVSVQAQILNL 540

Query: 200 LMQMKRQGIVKSIIFITHDIATVRQIADRMIIMYAGKIVEFAPVESLLEKPLHPYTQGLF 259
           L+ + R  +  + +F+TH+++ V+ +ADR+ +MY G+IVE    + ++  P HPYT  L 
Sbjct: 541 LLDL-RDELDLTYLFVTHNLSVVQHMADRVAVMYLGEIVECGERDQVMSDPKHPYTHALM 599

Query: 260 NSVL--TPEPEVKKRGITTIPGAPPNLINPPSGCRFHPRCPHAMDVCKEKEPPLTEIEPG 317
           NS L  +P   V   G++   G  PN +N PSGC FHPRCP A   C+E+ P   E+   
Sbjct: 600 NSALSISPGESVPDPGLS---GDFPNPMNRPSGCPFHPRCPLADQQCREQAPG-PELIDN 655

Query: 318 RRVACW 323
             V CW
Sbjct: 656 TLVQCW 661


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: 577
Number of extensions: 29
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: 672
Length adjustment: 33
Effective length of query: 297
Effective length of database: 639
Effective search space:   189783
Effective search space used:   189783
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