GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS03640 in Azospirillum brasilense Sp245

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate AZOBR_RS31880 AZOBR_RS31880 sugar ABC transporter ATP-binding protein

Query= uniprot:D8IZC7
         (521 letters)



>FitnessBrowser__azobra:AZOBR_RS31880
          Length = 515

 Score =  288 bits (737), Expect = 3e-82
 Identities = 175/490 (35%), Positives = 271/490 (55%), Gaps = 18/490 (3%)

Query: 1   MTQTPL-LQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPD 59
           MT  P+ L++ GI K FG  +A   + LT+  GE+ AL+GENGAGK+TLM +L G +  D
Sbjct: 1   MTSPPIVLRLSGITKRFGPLVANDSISLTLHKGEVLALLGENGAGKTTLMNILFGHYVAD 60

Query: 60  QGEILLDGRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAA 119
           +G I   G+P+    P A+ AAGI +++Q   +A N+SV  N+ +G+E   R    D AA
Sbjct: 61  EGSIEAFGQPLPPGSPRAALAAGIGMVHQHFTLADNLSVLDNIAVGTESLWR-PRSDRAA 119

Query: 120 MRSRTDAVLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERET 179
            +++   + R+ G       L G LS+ E+Q+ EI +AL   +R++I+DEPTA L+ +E+
Sbjct: 120 AKAKLLDLARRFGLEVRPDALVGDLSVGERQRAEILKALYRDARVLILDEPTAVLTPQES 179

Query: 180 EQLFNVVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMM 239
             LF+ +RRL  +GLA+++ISH+M EV+A +D V VLR G  V      E D E + ++M
Sbjct: 180 ASLFDTLRRLTADGLAVVFISHKMNEVFAASDTVAVLRGGRLVATRKTAETDREELAELM 239

Query: 240 VGRSLSEFYQHQRIAPADAAQLPTVMQVRALAGGKIRP----ASFDVRAGEVLGFAGLVG 295
           VGR+L    +     P +  +    +    +A G  RP        VR  +++G AG+ G
Sbjct: 240 VGRAL----KPPTPTPLEPGEPVLTLSGVTVASGHGRPLLDGVDLTVRRRQIVGIAGVSG 295

Query: 296 AGRTELARLLFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVA 355
            G+T LA L+ G      G + L+G  +   +P   +R G+A +PEDR   GL   MAV 
Sbjct: 296 NGQTALAELISGLIHPDSGTMTLKGEAIGNAEPAEMVRRGVARIPEDRHAAGLVGAMAVW 355

Query: 356 ANATMNVASRH-----TRLGLVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKV 410
            N    +A R+      R GL+R  +    A   I   +V+   P+     LSGGN QK+
Sbjct: 356 ENL---IAERYHDPAFQRFGLIRRGAARAYAEEVIAAFDVRCPGPDARTQLLSGGNMQKL 412

Query: 411 LLARWLEIAPKVLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDR 470
           +L R L   P +++  +PTRG+D+ A S ++  +    + G  V+VIS +L E++ + D 
Sbjct: 413 ILGRTLAHGPDLILASQPTRGLDVGAVSYVHGRLLEARAAGAGVLVISEDLDEILALADG 472

Query: 471 VLVMREGMIT 480
           + V   G +T
Sbjct: 473 ITVAYHGRLT 482



 Score = 92.0 bits (227), Expect = 5e-23
 Identities = 77/244 (31%), Positives = 113/244 (46%), Gaps = 20/244 (8%)

Query: 279 SFDVRAGEVLGFAGLVGAGRTELARLLFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAY 338
           S  +  GEVL   G  GAG+T L  +LFG      G I   G+P+    PRAA+ AGI  
Sbjct: 27  SLTLHKGEVLALLGENGAGKTTLMNILFGHYVADEGSIEAFGQPLPPGSPRAALAAGIGM 86

Query: 339 VPEDRKGQGLFLQMAVAANATMNVASRHTRLGLVRSRSLGGVARAAI----QRLNVKVAH 394
           V +      L   ++V  N  +   S      L R RS    A+A +    +R  ++V  
Sbjct: 87  VHQHFT---LADNLSVLDNIAVGTES------LWRPRSDRAAAKAKLLDLARRFGLEV-R 136

Query: 395 PETPVGKLSGGNQQKVLLARWLEIAPKVLILDEPTRGVDIYAKSEIYQLVHRLASQGVAV 454
           P+  VG LS G +Q+  + + L    +VLILDEPT  +     + ++  + RL + G+AV
Sbjct: 137 PDALVGDLSVGERQRAEILKALYRDARVLILDEPTAVLTPQESASLFDTLRRLTADGLAV 196

Query: 455 VVISSELPEVIGICDRVLVMREGMITGELAGAAITQENIMRLATDTNVPRTAPASHSSPT 514
           V IS ++ EV    D V V+R G +      A   +E +  L     +         +PT
Sbjct: 197 VFISHKMNEVFAASDTVAVLRGGRLVATRKTAETDREELAELMVGRAL------KPPTPT 250

Query: 515 PLAP 518
           PL P
Sbjct: 251 PLEP 254



 Score = 72.0 bits (175), Expect = 5e-17
 Identities = 59/245 (24%), Positives = 104/245 (42%), Gaps = 8/245 (3%)

Query: 5   PLLQMRGIRKSFGATLALSD-MHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEI 63
           P+L + G+  + G    L D + LT+R  +I  + G +G G++ L +++SG+  PD G +
Sbjct: 257 PVLTLSGVTVASGHGRPLLDGVDLTVRRRQIVGIAGVSGNGQTALAELISGLIHPDSGTM 316

Query: 64  LLDGRPVALRDPGASRAAGINLIYQELAVAPNISVAA---NVFMG---SELRTRLGLIDH 117
            L G  +   +P      G+  I ++   A  +   A   N+           R GLI  
Sbjct: 317 TLKGEAIGNAEPAEMVRRGVARIPEDRHAAGLVGAMAVWENLIAERYHDPAFQRFGLIRR 376

Query: 118 AAMRSRTDAVLRQLGAGFGASDLAGRL-SIAEQQQVEIARALVHRSRIVIMDEPTAALSE 176
            A R+  + V+          D   +L S    Q++ + R L H   +++  +PT  L  
Sbjct: 377 GAARAYAEEVIAAFDVRCPGPDARTQLLSGGNMQKLILGRTLAHGPDLILASQPTRGLDV 436

Query: 177 RETEQLFNVVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIV 236
                +   +   R  G  ++ IS  + E+ ALAD +TV   G     L    +   ++ 
Sbjct: 437 GAVSYVHGRLLEARAAGAGVLVISEDLDEILALADGITVAYHGRLTPVLPHGRVSVRQLG 496

Query: 237 QMMVG 241
            +M G
Sbjct: 497 LLMAG 501


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: 712
Number of extensions: 40
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: 515
Length adjustment: 35
Effective length of query: 486
Effective length of database: 480
Effective search space:   233280
Effective search space used:   233280
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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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:

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:

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:

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:

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