Alignments for a candidate for TM1749 in Marinobacter adhaerens HP15

GapMind for catabolism of small carbon sources

Alignments for a candidate for TM1749 in Marinobacter adhaerens HP15

Align TM1749, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized)
to candidate GFF2860 HP15_2804 oligopeptide/dipeptide ABC transporter, ATP-binding protein-like protein

Query= TCDB::Q9X271
         (324 letters)



>FitnessBrowser__Marino:GFF2860
          Length = 672

 Score =  279 bits (713), Expect = 2e-79
 Identities = 155/323 (47%), Positives = 201/323 (62%), Gaps = 10/323 (3%)

Query: 1   MMELLNVNNLKVEFHRVEGIVKAVDGISYKLNKGESLGIVGESGSGKSVSVLSLLRLI-- 58
           M  +L++ +L V+       + AV GIS +LN+GE+LGIVGESGSGKS++ L+L+ L+  
Sbjct: 3   MASILDIQDLSVDIPTDSSTLHAVRGISLELNRGETLGIVGESGSGKSMTALALMNLLPP 62

Query: 59  --NRNGRIVDGEAIFLGKDLLKLNKEELRN-IRGKDISIIFQNPMTSLNPIIRVGIQVME 115
              R    +D    F G DL    + EL + IRG+ I +IFQ PMTSLNP+  +G Q+ E
Sbjct: 63  AAKRQASCID----FDGSDLTHATERELASKIRGQRIGMIFQEPMTSLNPVYSIGRQLKE 118

Query: 116 PIIWHRLMKNEEARERAIELLERVGIPESPKRFLNYPFQFSGGMRQRVMIAMALACHPKL 175
            +  HR + + EA  RA+ LLE+VG+P+   R   YP + SGG RQRVMIAMAL   P+L
Sbjct: 119 TMTLHRKVSDTEAENRAVYLLEKVGLPDPASRLKQYPHELSGGQRQRVMIAMALMNEPEL 178

Query: 176 LIADEPTTALDVTIQAQIMELLQELKEEYGMSVIFITHDLSVATNFCDRIITMYAGKIVE 235
           LIADEPTTALDVTIQAQI+ LL+EL++E+GMS+I ITHDL V +   D I  MYAG IVE
Sbjct: 179 LIADEPTTALDVTIQAQILHLLRELQQEFGMSMILITHDLGVVSRAADNIAVMYAGDIVE 238

Query: 236 EAPVEEILKTPLHPYTKGLLNSTLEI-GSRGKKLVPIPGNPPNPTKHPSGCKFHPRCSFA 294
                E+L+ P HPYTKGLL       G   ++L  IPG  P  T   SGC F  RC  A
Sbjct: 239 TGKTGEVLENPRHPYTKGLLECVPGYKGQSQQRLGAIPGIVPAMTGDISGCAFASRCPRA 298

Query: 295 MEICQREEPPLVNISENHRVACH 317
             +C+   PP   + +     CH
Sbjct: 299 AGVCRTTNPPTKKLHQGRYFVCH 321



 Score =  209 bits (532), Expect = 2e-58
 Identities = 125/327 (38%), Positives = 192/327 (58%), Gaps = 30/327 (9%)

Query: 3   ELLNVNNLKVEFHRVEGI------VKAVDGISYKLNKGESLGIVGESGSGKSVSVLSLLR 56
           ++L V+++   F    G+      ++A+D +S  L KGE L +VGESG GK+    +++ 
Sbjct: 351 DILTVDHVSCTFSVRRGMFGKRKPLQALDDVSLTLKKGEVLALVGESGCGKTTLTRTIMG 410

Query: 57  LINRNGRIVDGEAIFLGKDLLKLNKEELRNI----RGKDISIIFQNPMTSLNPIIRVGIQ 112
           L          +A   G   + LN + + N+    R + I  IFQ+P +SLNP   +G  
Sbjct: 411 L----------QAPSTGS--VTLNGQRIENLPPMDRARMIQPIFQDPYSSLNPRKTIGEI 458

Query: 113 VMEPIIWHRLMKNEEARERAIELLERVGIPESPKRFLNYPFQFSGGMRQRVMIAMALACH 172
           + +P+  H +  N+E  ++  +++E VG+P   + F +YP Q SGG RQR  I  AL  +
Sbjct: 459 IAKPLFVHGIGSNQEQHQQVRKMMELVGLPS--RVFNSYPDQLSGGQRQRAAIGRALILN 516

Query: 173 PKLLIADEPTTALDVTIQAQIMELLQELKEEYGMSVIFITHDLSVATNFCDRIITMYAGK 232
           P+++I DEPT+ALDV++QAQI+ LL +L++E  ++ +F+TH+LSV  +  DR+  MY G+
Sbjct: 517 PEVVICDEPTSALDVSVQAQILNLLLDLRDELDLTYLFVTHNLSVVQHMADRVAVMYLGE 576

Query: 233 IVEEAPVEEILKTPLHPYTKGLLNSTLEIGSRGKKLVPIP---GNPPNPTKHPSGCKFHP 289
           IVE    ++++  P HPYT  L+NS L I S G+  VP P   G+ PNP   PSGC FHP
Sbjct: 577 IVECGERDQVMSDPKHPYTHALMNSALSI-SPGES-VPDPGLSGDFPNPMNRPSGCPFHP 634

Query: 290 RCSFAMEICQREEPPLVNISENHRVAC 316
           RC  A + C RE+ P   + +N  V C
Sbjct: 635 RCPLADQQC-REQAPGPELIDNTLVQC 660


Lambda     K      H
   0.320    0.139    0.401 

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: 572
Number of extensions: 28
Number of successful extensions: 7
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: 324
Length of database: 672
Length adjustment: 33
Effective length of query: 291
Effective length of database: 639
Effective search space:   185949
Effective search space used:   185949
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