Alignments for a candidate for HSERO_RS03640 in Azospirillum brasilense Sp245

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 Apr 09 2024. 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 2024 update 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