Alignments for a candidate for HSERO_RS03640 in Lacinutrix himadriensis E4-9a

GapMind for catabolism of small carbon sources

Alignments for a candidate for HSERO_RS03640 in Lacinutrix himadriensis E4-9a

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate WP_055444834.1 AMD28_RS14385 sugar ABC transporter ATP-binding protein

Query= uniprot:D8IZC7
         (521 letters)



>NCBI__GCF_001418105.1:WP_055444834.1
          Length = 506

 Score =  388 bits (997), Expect = e-112
 Identities = 205/492 (41%), Positives = 315/492 (64%), Gaps = 8/492 (1%)

Query: 7   LQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILLD 66
           L+M GI KSFG    L +++L ++ GEIHAL+GENGAGKSTL+K+LSGVH  D G ++LD
Sbjct: 10  LEMTGISKSFGVVSVLKNVNLKVKSGEIHALLGENGAGKSTLIKILSGVHQKDTGTVVLD 69

Query: 67  GRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAAMRSRTDA 126
           G+ +  ++    +  GIN++YQEL++  ++SVA N+++  +L      ++   +      
Sbjct: 70  GQEITPKNTHEGQVLGINVVYQELSLVNDLSVAENIYL-HKLGANKTWMNWKGLIKDAQE 128

Query: 127 VLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFNVV 186
           +L  L     AS     LSI ++Q VEIA+A+   ++I+I+DEPT     ++ ++LFN++
Sbjct: 129 LLDSLDFKINASAKVKDLSIVQKQVVEIAKAISEDTKILILDEPTTVFDPKDVKKLFNIL 188

Query: 187 RRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVGRSLSE 246
            +L+++G +IIYISH + E++ +AD VTVLRDG   G L   + D + ++ +M+GR L +
Sbjct: 189 FKLKEKGTSIIYISHHLDEIFKIADSVTVLRDGVDTGSLAIADTDKDGVIHLMIGRELKD 248

Query: 247 FYQHQRIAPADAAQLPTVMQVRALAGGK--IRPASFDVRAGEVLGFAGLVGAGRTELARL 304
            Y  + +   +      + +V+ L      +   SF V+ GEVLG AGL G+GRTE A+L
Sbjct: 249 LYPKRDVKIGEVP----IFEVKNLTAKDTMVHDVSFHVKPGEVLGIAGLGGSGRTETAKL 304

Query: 305 LFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAANATM-NVA 363
           +FGAD +  G ++LEG+ +  + P  A R  I +V EDRK +G+FL +++  N ++ +  
Sbjct: 305 IFGADKKKSGTLILEGKEIVTNSPVDAARYQIGFVSEDRKEEGVFLPLSIRRNISVTSFD 364

Query: 364 SRHTRLGLVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWLEIAPKVL 423
           S  ++LG +   S        I++LN+K  + E  V  LSGGNQQKV LA+WL I  KV+
Sbjct: 365 SISSKLGFINVESEYKKVLGLIEKLNIKTPNSEINVKNLSGGNQQKVALAKWLSIESKVI 424

Query: 424 ILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVMREGMITGEL 483
            +DEPTRGVD+ AK EIY+L++ +A +GV VVVISS++PE++GI DR+LVM EG   GEL
Sbjct: 425 FIDEPTRGVDVGAKIEIYKLINEVAKKGVGVVVISSDMPEIMGISDRILVMHEGTFYGEL 484

Query: 484 AGAAITQENIMR 495
                ++ENI+R
Sbjct: 485 PKEKFSEENILR 496



 Score = 95.1 bits (235), Expect = 5e-24
 Identities = 53/227 (23%), Positives = 117/227 (51%), Gaps = 6/227 (2%)

Query: 24  DMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILLDGRPVALRDPGASRAAGI 83
           D+   ++PGE+  + G  G+G++   K++ G      G ++L+G+ +    P  +    I
Sbjct: 277 DVSFHVKPGEVLGIAGLGGSGRTETAKLIFGADKKKSGTLILEGKEIVTNSPVDAARYQI 336

Query: 84  NLIYQ---ELAVAPNISVAANVFMGS--ELRTRLGLIDHAAMRSRTDAVLRQLGAGFGAS 138
             + +   E  V   +S+  N+ + S   + ++LG I+  +   +   ++ +L      S
Sbjct: 337 GFVSEDRKEEGVFLPLSIRRNISVTSFDSISSKLGFINVESEYKKVLGLIEKLNIKTPNS 396

Query: 139 DL-AGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFNVVRRLRDEGLAII 197
           ++    LS   QQ+V +A+ L   S+++ +DEPT  +      +++ ++  +  +G+ ++
Sbjct: 397 EINVKNLSGGNQQKVALAKWLSIESKVIFIDEPTRGVDVGAKIEIYKLINEVAKKGVGVV 456

Query: 198 YISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVGRSL 244
            IS  M E+  ++DR+ V+ +G+F GEL +++   E I++  +G  L
Sbjct: 457 VISSDMPEIMGISDRILVMHEGTFYGELPKEKFSEENILRYSIGEPL 503



 Score = 79.3 bits (194), Expect = 3e-19
 Identities = 59/226 (26%), Positives = 114/226 (50%), Gaps = 14/226 (6%)

Query: 275 IRPASFDVRAGEVLGFAGLVGAGRTELARLLFGADPRSGGDILLEGRPVHIDQPRAAMRA 334
           ++  +  V++GE+    G  GAG++ L ++L G   +  G ++L+G+ +           
Sbjct: 25  LKNVNLKVKSGEIHALLGENGAGKSTLIKILSGVHQKDTGTVVLDGQEITPKNTHEGQVL 84

Query: 335 GIAYVPEDRKGQGLFLQMAVAANATMN-VASRHTRL---GLVRSRSLGGVARAAIQRLNV 390
           GI  V ++     L   ++VA N  ++ + +  T +   GL++       A+  +  L+ 
Sbjct: 85  GINVVYQELS---LVNDLSVAENIYLHKLGANKTWMNWKGLIKD------AQELLDSLDF 135

Query: 391 KVAHPETPVGKLSGGNQQKVLLARWLEIAPKVLILDEPTRGVDIYAKSEIYQLVHRLASQ 450
           K+ +    V  LS   +Q V +A+ +    K+LILDEPT   D     +++ ++ +L  +
Sbjct: 136 KI-NASAKVKDLSIVQKQVVEIAKAISEDTKILILDEPTTVFDPKDVKKLFNILFKLKEK 194

Query: 451 GVAVVVISSELPEVIGICDRVLVMREGMITGELAGAAITQENIMRL 496
           G +++ IS  L E+  I D V V+R+G+ TG LA A   ++ ++ L
Sbjct: 195 GTSIIYISHHLDEIFKIADSVTVLRDGVDTGSLAIADTDKDGVIHL 240


Lambda     K      H
   0.320    0.135    0.378 

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: 602
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: 3
Length of query: 521
Length of database: 506
Length adjustment: 35
Effective length of query: 486
Effective length of database: 471
Effective search space:   228906
Effective search space used:   228906
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 24 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:

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