Alignments for a candidate for cbtD in Marinobacter adhaerens HP15

GapMind for catabolism of small carbon sources

Alignments for a candidate for cbtD in Marinobacter adhaerens HP15

Align CbtD, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate GFF2860 HP15_2804 oligopeptide/dipeptide ABC transporter, ATP-binding protein-like protein

Query= TCDB::Q97VF5
         (362 letters)



>FitnessBrowser__Marino:GFF2860
          Length = 672

 Score =  189 bits (481), Expect = 1e-52
 Identities = 112/317 (35%), Positives = 183/317 (57%), Gaps = 7/317 (2%)

Query: 45  ILEVHNLNVIYDEGNSRIIKAVNDVSFGVEKGEILGIIGESGSGKTTLISAILRAIRPPG 104
           IL++ +L+V     +S +  AV  +S  + +GE LGI+GESGSGK+    A++  + P  
Sbjct: 6   ILDIQDLSVDIPTDSSTL-HAVRGISLELNRGETLGIVGESGSGKSMTALALMNLLPPAA 64

Query: 105 KIISGKVIFNGMDIFSMTIDEFR-KLLWKDISYVPQASQNALNPVLPISEIFYHEAISHG 163
           K  +  + F+G D+   T  E   K+  + I  + Q    +LNPV  I          H 
Sbjct: 65  KRQASCIDFDGSDLTHATERELASKIRGQRIGMIFQEPMTSLNPVYSIGRQLKETMTLHR 124

Query: 164 EADKKRVIERASELLKLVGL-DPARVLKMYPFQLSGGMKQRVMIALSLLLNPKLILMDEP 222
           +        RA  LL+ VGL DPA  LK YP +LSGG +QRVMIA++L+  P+L++ DEP
Sbjct: 125 KVSDTEAENRAVYLLEKVGLPDPASRLKQYPHELSGGQRQRVMIAMALMNEPELLIADEP 184

Query: 223 TSALDMLNQELLLKLIKNINQEMGVTIVYVTHDILNIAQIANRLLVMYKGYVMEEGKTEE 282
           T+ALD+  Q  +L L++ + QE G++++ +THD+  +++ A+ + VMY G ++E GKT E
Sbjct: 185 TTALDVTIQAQILHLLRELQQEFGMSMILITHDLGVVSRAADNIAVMYAGDIVETGKTGE 244

Query: 283 IIKSPLNPYTSLLVSSIPSLKG--EVKVINVPLDEPLVSKE-KGCPFLARCSKAFGRCKE 339
           ++++P +PYT  L+  +P  KG  + ++  +P   P ++ +  GC F +RC +A G C+ 
Sbjct: 245 VLENPRHPYTKGLLECVPGYKGQSQQRLGAIPGIVPAMTGDISGCAFASRCPRAAGVCRT 304

Query: 340 ELPEIRLVYD-RKVRCH 355
             P  + ++  R   CH
Sbjct: 305 TNPPTKKLHQGRYFVCH 321



 Score =  176 bits (447), Expect = 1e-48
 Identities = 102/300 (34%), Positives = 173/300 (57%), Gaps = 12/300 (4%)

Query: 58  GNSRIIKAVNDVSFGVEKGEILGIIGESGSGKTTLISAILRAIRPPGKIISGKVIFNGMD 117
           G  + ++A++DVS  ++KGE+L ++GESG GKTTL   I+    P     +G V  NG  
Sbjct: 370 GKRKPLQALDDVSLTLKKGEVLALVGESGCGKTTLTRTIMGLQAPS----TGSVTLNGQR 425

Query: 118 IFSMTIDEFRKLLWKDISYVPQASQNALNPVLPISEIFYHEAISHGEADKKRVIERASEL 177
           I ++   +  ++    I  + Q   ++LNP   I EI       HG    +   ++  ++
Sbjct: 426 IENLPPMDRARM----IQPIFQDPYSSLNPRKTIGEIIAKPLFVHGIGSNQEQHQQVRKM 481

Query: 178 LKLVGLDPARVLKMYPFQLSGGMKQRVMIALSLLLNPKLILMDEPTSALDMLNQELLLKL 237
           ++LVGL P+RV   YP QLSGG +QR  I  +L+LNP++++ DEPTSALD+  Q  +L L
Sbjct: 482 MELVGL-PSRVFNSYPDQLSGGQRQRAAIGRALILNPEVVICDEPTSALDVSVQAQILNL 540

Query: 238 IKNINQEMGVTIVYVTHDILNIAQIANRLLVMYKGYVMEEGKTEEIIKSPLNPYTSLLVS 297
           + ++  E+ +T ++VTH++  +  +A+R+ VMY G ++E G+ ++++  P +PYT  L++
Sbjct: 541 LLDLRDELDLTYLFVTHNLSVVQHMADRVAVMYLGEIVECGERDQVMSDPKHPYTHALMN 600

Query: 298 SIPSLKGEVKVINVPLDEPL---VSKEKGCPFLARCSKAFGRCKEELPEIRLVYDRKVRC 354
           S  S+     V +  L       +++  GCPF  RC  A  +C+E+ P   L+ +  V+C
Sbjct: 601 SALSISPGESVPDPGLSGDFPNPMNRPSGCPFHPRCPLADQQCREQAPGPELIDNTLVQC 660


Lambda     K      H
   0.319    0.138    0.391 

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: 512
Number of extensions: 22
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 2
Length of query: 362
Length of database: 672
Length adjustment: 34
Effective length of query: 328
Effective length of database: 638
Effective search space:   209264
Effective search space used:   209264
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: 52 (24.6 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