Alignments for a candidate for TM1750 in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for TM1750 in Herbaspirillum seropedicae SmR1

Align TM1750, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized)
to candidate HSERO_RS09190 HSERO_RS09190 ABC transporter ATP-binding protein

Query= TCDB::Q9X272
         (328 letters)



>FitnessBrowser__HerbieS:HSERO_RS09190
          Length = 617

 Score =  266 bits (679), Expect = 1e-75
 Identities = 151/321 (47%), Positives = 211/321 (65%), Gaps = 25/321 (7%)

Query: 8   IKMKPLLQTVDLKK-YFPQGKRILKAVDGISIEIKEGETLGLVGESGCGKSTLGRTILKL 66
           +K++ L    D+K   F + ++ + AV+ +S ++  GETL +VGESGCGKST GR++L+L
Sbjct: 313 LKVRDLTTRFDVKSGIFGRVRQRVHAVEKVSFDLYAGETLAIVGESGCGKSTTGRSLLRL 372

Query: 67  LRPDGGKIFFEGKDITNLNDKEMKPYRKKMQIIFQDPLGSLNPQMTVGRIIEDPLIIHKI 126
           +   GGK+ F G+D+  L   E++  R+ +Q IFQDP  SL+P+MTVG  I +P+++H  
Sbjct: 373 VDIAGGKVEFGGRDLAQLPRSELRQLRRDIQFIFQDPFASLDPRMTVGYSIMEPMLVH-- 430

Query: 127 GTKKERRKRVEELLDMVGIGREFINSFPHEFSGGQQQRIGIARALALNPKFIVCDEPVSA 186
           G K+  ++RV+ LL  VG+  E    +PHEFSGGQ+QRI IARALALNPK ++ DE VSA
Sbjct: 431 GMKEGAQERVDALLTRVGLTPEHGQRYPHEFSGGQRQRICIARALALNPKIVIADESVSA 490

Query: 187 LDVSIQAQIIDLLEEIQQKMGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVDKIFL 246
           LDVSIQAQI++L+ ++Q ++GIS++FI+H++AVVE ISH+VAVMYLG+IVE G    IF 
Sbjct: 491 LDVSIQAQIVNLMLDLQAELGISFIFISHDMAVVERISHRVAVMYLGQIVEIGPRRAIFE 550

Query: 247 NPIHPYTRALLKSVPKIPWDGQKQRFYSLKGELPSPI----DLPKGCRFQTRCTEKKAIC 302
           NP HPYTR L+ +VP      ++     L  E+PSPI    D PK               
Sbjct: 551 NPQHPYTRKLMAAVPVADPTLRQPGKKLLTDEIPSPIRRVGDEPK--------------- 595

Query: 303 FEKEPELTEVEKNHFVSCHLV 323
              EP L EV   HFV+ H +
Sbjct: 596 --VEP-LQEVAPGHFVAQHRI 613



 Score =  170 bits (430), Expect = 1e-46
 Identities = 95/264 (35%), Positives = 152/264 (57%), Gaps = 13/264 (4%)

Query: 13  LLQTVDLKKYFPQGKRILKAVDGISIEIKEGETLGLVGESGCGKSTLGRTILKLLRPDGG 72
           +L    L   F   +R + AV  +S  + +GETL +VGESG GKS     I++L+   GG
Sbjct: 7   VLDVNHLSVRFSTSERTVDAVRDLSFHVDQGETLAIVGESGSGKSVSSLAIMRLIEHGGG 66

Query: 73  KIFF----------EGKDITNLNDKEMKPYR-KKMQIIFQDPLGSLNPQMTVGRIIEDPL 121
           KI            +  D+   ++  M+  R  ++ +IFQ+P+ SLNP  TVG  I + +
Sbjct: 67  KIASGSMQFLRRSGQRLDLAQADNATMRSIRGAEIAMIFQEPMTSLNPVFTVGEQIAESI 126

Query: 122 IIHKIGTKKERRKRVEELLDMVGI--GREFINSFPHEFSGGQQQRIGIARALALNPKFIV 179
            +H+   +   +     +L+MV I   +  +   PH+ SGG +QR+ IA AL+  P  ++
Sbjct: 127 RLHQGLGRAAAQAEALRMLEMVRIPEAKRVLGRHPHQLSGGMRQRVMIAMALSCKPSLLI 186

Query: 180 CDEPVSALDVSIQAQIIDLLEEIQQKMGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYG 239
            DEP +ALDV+IQAQI+ L+  +QQ+M +  +FI H++ VV  ++ +V VM  G+ VE  
Sbjct: 187 ADEPTTALDVTIQAQILQLIRSLQQEMQMGVIFITHDMGVVAEVADRVVVMCRGEKVEEN 246

Query: 240 DVDKIFLNPIHPYTRALLKSVPKI 263
            V+ +F  P HPYT++LL +VP++
Sbjct: 247 AVNPLFAAPAHPYTQSLLAAVPRL 270


Lambda     K      H
   0.321    0.142    0.417 

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: 607
Number of extensions: 34
Number of successful extensions: 5
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: 328
Length of database: 617
Length adjustment: 33
Effective length of query: 295
Effective length of database: 584
Effective search space:   172280
Effective search space used:   172280
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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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